BOL: Related items

Computer simulation of genetic mechanism !!

Jit — Sun, 13 Mar 2016 09:29:56 -0500

Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output. Simulation embodies the principle of ``learning by doing'' --- to learn about the system we must first build a model of some sort and then operate the model. The use of simulation is an activity that is as natural as a child who role plays. Children understand the world around them by simulating (with toys and figurines) most of their interactions with other people, animals and objects. As adults, we lose some of this childlike behavior but recapture it later on through computer simulation. To understand reality and all of its complexity, we must build artificial objects and dynamically act out roles with them. Computer simulation is the electronic equivalent of this type of role playing and it serves to drive synthetic environments and virtual worlds. Within the overall task of simulation, there are three primary sub-fields: model design, model execution and model analysis

Simulation models have become important tools in Bioinformatics studies. There are many reasons for this, but we emphasize three of the more important:

(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;

(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and

(3) they enable connecting biology with other fields of study ranging from physiology to genomics;

This blog, and this software list, is intended to guide the potential user of simulation models.
It is not, in any way, meant to be comprehensive on the very diverse simulation tools that already exist, but focuses on mechanistic, dynamic models. Similarly, it is not meant to provide any coverage of the breadth of applications; however, for interested readers, we provide references to use as a possible starting point.

Simulation models are meant to answer questions which scientists have in a dynamic, quantitative, and often, a pictorial way. Much of the bioinformatics research and its applications, in particular, involve a large number of components, actors, and factors. Assembling these in a coherent framework may seem a daunting task, especially for beginners, and can lead to confusion, even for experienced scientists, especially if the objectives of such an exercise are not well defined. Followings are the list of tools bioinformatician may use to analyze and provide answers to complex biological mechanisms and related problems.

Software Resource	Brief Description and Homepage
Aladyn	Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation http://www.katja-schiffers.eu/research.html
ALF	A Simulation Framework for Genome Evolution http://www.cbrg.ethz.ch/alf
ART	ART is a set of simulation tools to generate synthetic next-generation sequencing data by mimicking real sequencing process with empirical error models or quality profiles. http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
BAMSurgeon	Methods for realistic simulation of mutations in real data. https://github.com/adamewing/bamsurgeon
Bayesian Serial SimCoal	Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. http://www.stanford.edu/group/hadlylab/ssc/index.html
BaySICS	An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation. https://sites.google.com/site/baysicsabc/
BEERS	BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data http://cbil.upenn.edu/beers/
BOTTLENECK	Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html
BottleSim	BottleSim is a computer simulation program for simulating the process of population bottlenecks http://chkuo.name/software/bottlesim.html
CASS	Protein Sequence Simulation https://liberles.cst.temple.edu/software/cass/index.html
CDPOP	CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. http://cel.dbs.umt.edu/cdpop
Classical Genetics Simulator	Web-based simulation software http://www.cgslab.com/
CoaSim	CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. http://users-birc.au.dk/mailund/coasim/index.html
cosi	The cosi package is written in C and is available as a tar file. http://www.broadinstitute.org/~sfs/cosi/
CS-PSeq-Gen	A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen/
DAWG	An application designed to simulate the evolution of recombinant DNA sequences in continuous time http://scit.us/projects/dawg
Easypop	EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html
EggLib	EggLib is a C++/Python library and program package for evolutionary genetics and genomics. http://egglib.sourceforge.net/
EpiSIM	EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis https://sourceforge.net/projects/episimsimulator/files/
EvolSimulator	A simulation test bed for hypotheses of genome evolution http://acb.qfab.org/acb/evolsim/
EvolveAGene	A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions http://bellinghamresearchinstitute.com/software/index.html
fastsimcoal	A continuous-‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios http://cmpg.unibe.ch/software/fastsimcoal/
FastSLINK	Simulation of Marker and Phenotype Data in Pedigrees https://watson.hgen.pitt.edu/
FFPopSim	C++/Python library for population genetics. http://webdav.tuebingen.mpg.de/ffpopsim/
FLUX SIMULATOR	The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. http://sammeth.net/confluence/display/sim/home
forqs	Forward-in-time simulation of Recombination, Quantitative Traits, and Selection https://bitbucket.org/dkessner/forqs
ForSim	ForSim: A Forward Evolutionary Computer Simulation http://anth.la.psu.edu/research/weiss-lab/research/research
ForwSim	The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. http://badri-populationgeneticsimulators.blogspot.com/
FPG	Forward Population Genetic simulation https://bio.cst.temple.edu/~hey/software/software.htm#fpg
FREGENE	FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.ac.uk/projects/bargen
FIGG	FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied mutations for use in analysis http://insilicogenome.sourceforge.net/
fwdpp	A C++ template library for implementing efficient forward simulations. http://molpopgen.github.io/fwdpp/
GAMETES	Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. http://sourceforge.net/projects/gametes/?source=navbar
GASP	Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. http://research.nhgri.nih.gov/gasp/
GCTA	Genome-wide Complex Trait Analysis http://www.complextraitgenomics.com/software/gcta/download.html
GemSIM	Next generation sequencing read simulator http://sourceforge.net/projects/gemsim/
GeneArtisan	Simulation of Markers in Case-Control Study Designs http://www.rannala.org/?page_id=241
GENOME	A rapid coalescent-based whole genome simulator http://www.sph.umich.edu/csg/liang/genome/
GenomePop2	GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla
GenomeSimla	GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested http://chgr.mc.vanderbilt.edu/genomesimla/
GENS2	Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. https://sourceforge.net/projects/gensim/
GWAsimulator	A rapid whole genome simulation program http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator
HAP-SAMPLE	An association simulator for candidate regions or genome scans http://www.hapsample.org/
HAPGEN	A simulator for the simulation of case control datasets at SNP markers https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
HapSim	A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients http://cran.r-project.org/web/packages/hapsim/index.html
HAPSIMU	A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model http://l.web.umkc.edu/liujian/
IBDsim	IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. http://raphael.leblois.free.fr/
indel-Seq-Gen	A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies http://bioinfolab.unl.edu/~cstrope/isg/
Indelible	A powerful and flexible simulator of biological evolution http://abacus.gene.ucl.ac.uk/software/indelible/
invertFREGENE	InvertFREGENE is a forward-in-time simulator of inversions in population genetic data http://www.ebi.ac.uk/projects/bargen/
kernalPop	A spatially explicit population genetic simulation engine http://cran.r-project.org/src/contrib/archive/kernelpop/
MaCS	Markovian Coalescent Simulator http://www-hsc.usc.edu/~garykche/
Marlin	Marlin provides a user-friendly interface for performing forward-in-time population genetic simulations. http://www.patrickmeirmans.com/software/marlin.html
Mason	A package for the simulation of nucleotide data. http://www.seqan.de/projects/mason/
mbs	modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html
Mendel's Accountant	Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine http://mendelsaccount.sourceforge.net/
MetaPopGen	Simulates genetics in large size metapopulations https://sites.google.com/site/marcoandrello/metapopgen
MetaSim	A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets http://ab.inf.uni-tuebingen.de/software/metasim/
mlcoalsim	Multilocus Coalescent Simulations http://code.google.com/p/mlcoalsim-v1/
ms	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/source/mksamples.html
msHOT	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/
msms	A coalescent Simlation tool with selection. http://www.mabs.at/ewing/msms/index.shtml
MySSP	A program for the simulation of DNA sequence evolution across a phylogenetic tree http://www.rosenberglab.net/software.html
Nemo	A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. http://nemo2.sourceforge.net/
NetRecodon	Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography http://code.google.com/p/netrecodon/
OncoSimulR	BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis https://github.com/rdiaz02/oncosimul
PEDAGOG	Software for simulating eco-evolutionary population dynamics https://bcrc.bio.umass.edu/pedigreesoftware/node/5
phenosim	A tool to add phenotypes to simulated genotypes http://evoplant.uni-hohenheim.de/doku.php?id=software:software
PhyloSim	An R package for the Monte Carlo simulation of sequence evolution http://www.ebi.ac.uk/goldman-srv/phylosim/
pIRS	Profile-based Illumina pair-end reads simulator https://code.google.com/p/pirs/
ProteinEvolver	Simulation of protein evolution along phylogenies under structure-based substitution models http://code.google.com/p/proteinevolver/
QMSim	QTL and Marker Simulator http://www.aps.uoguelph.ca/~msargol/qmsim/
quantiNEMO	An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population http://www2.unil.ch/popgen/softwares/quantinemo/
RECOAL	Simulates new haplotype data from a reference population of haplotypes. ftp://popgen.usc.edu/
Recodon	Coalescent simulation of coding DNA sequences with recombination, migration and demography http://code.google.com/p/recodon/
rlsim	A package for simulating RNA-seq library preparation with parameter estimation http://bit.ly/rlsim-git
Rmetasim	Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R http://cran.r-project.org/web/packages/rmetasim/index.html
RNA Seq Simulator	RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator
Rose	Random model of sequence evolution http://bibiserv.techfak.uni-bielefeld.de/rose/
scrm	A coalescent simulator optimized for long sequences and large samples. https://scrm.github.io/
SelSim	SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection http://www.well.ox.ac.uk/~spencer/selsim/
Seq-Gen	An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. http://tree.bio.ed.ac.uk/software/seqgen/
SEQPower	Statistical power analysis for sequence-based association studies http://bioinformatics.org/spower/
SeqSIMLA	SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. http://seqsimla.sourceforge.net/
Serial NetEvolve	A flexible utility for generating serially-sampled sequences along a tree or recombinant network http://biorg.cis.fiu.edu/sne/
SFS_CODE	SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. http://sfscode.sourceforge.net/sfs_code/index/index.html
SIBSIM	Quantitative phenotype simulation in extended pedigrees http://sourceforge.net/projects/sibsim/
SimAdapt	A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton. https://www.openabm.org/model/3137
SIMCOAL2	A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models http://cmpg.unibe.ch/software/simcoal2/
SimCopy	An R package simulating the evolution of copy number profiles along a tree. http://bit.ly/simcopy
SIMLA	SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. http://dmpi.duke.edu/simla-simulation-software-version-32
SimPed	A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures http://bioinformatics.org/simped/
Simprot	A program to simulate protein evolution by substitution, insertion and deletion http://www.uhnresearch.ca/labs/tillier/software.htm#3
SimRare	Rare variant simulation and analysis tool http://code.google.com/p/simrare/
simuGWAS	A forward-time simulator that simulates realistic samples for genome-wide association studies. http://simupop.sourceforge.net/cookbook/simugwas
simuPOP	simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. http://simupop.sourceforge.net/
SISSI	A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. http://www.cibiv.at/software/sissi/
SMARTPOP	Simulating Mating Alliance as a Reproductive Tactic for Populations http://smartpop.sourceforge.net/
SNPsim	Coalescent simulation of hotspot recombination http://code.google.com/p/phylosoftware/
SPIP	SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user http://swfsc.noaa.gov/textblock.aspx?division=fed&id=3434
Splatche	Spatial and Temporal Coalescences in Heterogeneous Environment http://www.splatche.com/
srv	Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. http://simupop.sourceforge.net/cookbook/simurarevariants
SUP	SLINK/FastSLINK utility program http://mlemire.freeshell.org/software.html
TreesimJ	A flexible, forward-time population genetic simulator http://code.google.com/p/treesimj/
Variant Simulation Tools	A simulation tool for post-GWAS genetic epidemiological studies using whole-genome or whole-exome next-gen sequencing data, with an emphasis on user-friendliness and reproducibility. http://varianttools.sourceforge.net/simulation/homepage
Vortex	VORTEX is an individual-based simulation model for population viability analysis (PVA). http://www.vortex9.org/vortex.html
Wessim	Whole Exome Sequencing SIMulator http://sak042.github.io/wessim/

Stand-alone programs for Bioinformatician

Radha Agarkar — Sat, 21 May 2016 22:50:15 -0500

This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine.

For help on the bigBed and bigWig applications see:
http://genome.ucsc.edu/goldenPath/help/bigBed.html
http://genome.ucsc.edu/goldenPath/help/bigWig.html

View the file 'FOOTER' to see the usage statement for each of the applications.

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Useful Bioinformatics Tools

Poonam Mahapatra — Mon, 29 Aug 2016 04:08:12 -0500

Collections of few handy tools for bioinformatician

http://molbiol-tools.ca/Convert.htm

Address of the bookmark: http://molbiol-tools.ca/Convert.htm

Harvest

Jit — Tue, 31 Jan 2017 10:57:56 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

Tools for bacterial whole genome annotation

Radha Agarkar — Sat, 16 Dec 2017 17:37:47 -0600

RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation (if you have only a few genomes to annotate).

Prokka – Standalone command line tool, takes just a few minutes per genome. This is the best way to get good quality annotation in a flash, which is particularly useful if you have loads of genomes or need to annotate a pangenome or metagenome. Note however that the quality of functional information is not as good as RAST, and you will need several extra steps if you want to do functional profiling and pathway analysis of your genome(s)… which is in-built in RAST.

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

PGAP: NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

BEACON (automated tool for Bacterial GEnome Annotation ComparisON), a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.

BlastKOLA: Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to this server and can be executed in an interactive mode. BlastKOALA is suitable for annotating fully sequenced genomes.

PAGIT: Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.

MAKER: A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).

MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

Installing python-numpy !

Jit — Mon, 07 May 2018 04:31:25 -0500

$ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
[sudo] password for urbe:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic
linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic
linux-signed-image-4.4.0-116-generic runc ubuntu-fan
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
blt fonts-lyx fonts-mathjax ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2 libhdf5-10 libjs-highlight
libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4 python-chardet python-cvxopt
python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging python-jdcal python-jinja2 python-joblib
python-lxml python-markupsafe python-matplotlib-data python-mpmath python-numexpr python-openpyxl python-pandas-lib python-patsy python-pexpect
python-pil python-ptyprocess python-py python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-simplegeneric
python-simplejson python-statsmodels python-statsmodels-lib python-sympy-doc python-tables python-tables-data python-tables-lib python-tk
python-tornado python-tz python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
Suggested packages:
blt-demo ipython-doc ipython-qtconsole python-pygments nodejs pandoc libiodbc2-dev libmysqlclient-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras libjs-mathjax-doc python-gtk2-doc python-genshi python-jinja2-doc python-lxml-dbg
python-lxml-doc ffmpeg inkscape python-cairocffi python-configobj python-excelerator python-matplotlib-doc python-qt4 python-sip python-traits
python-wxgtk3.0 ttf-staypuft python-gmpy2 python-mpmath-doc python-coverage python-nose-doc python-numpy-dbg python-numpy-doc python-pandas-doc
python-patsy-doc python-pexpect-doc python-pil-doc python-pil-dbg subversion python-pytest-xdist libcurl4-gnutls-dev python-pycurl-dbg
python-pycurl-doc python-pymysql-doc python-mock python-scipy-doc python-statsmodels-doc python-tables-doc python-netcdf vitables tix
python-tk-dbg
The following NEW packages will be installed:
blt fonts-lyx fonts-mathjax ipython ipython-notebook ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2
libhdf5-10 libjs-highlight libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4
python-chardet python-cvxopt python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging
python-jdcal python-jinja2 python-joblib python-lxml python-markupsafe python-matplotlib python-matplotlib-data python-mpmath python-nose
python-numexpr python-numpy python-openpyxl python-pandas python-pandas-lib python-patsy python-pexpect python-pil python-ptyprocess python-py
python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-scipy python-simplegeneric python-simplejson python-statsmodels
python-statsmodels-lib python-sympy python-sympy-doc python-tables python-tables-data python-tables-lib python-tk python-tornado python-tz
python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
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Get:12 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-highlight all 8.2+ds-4build1 [7.032 B]
Get:13 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-jquery-ui all 1.10.1+dfsg-1 [458 kB]
Get:14 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-marked all 0.3.2+dfsg-1 [12,7 kB]
Get:15 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libjs-mathjax all 2.6.1-1 [5.601 kB]
Get:16 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 libjs-underscore all 1.7.0~dfsg-1ubuntu1 [46,7 kB]
Get:17 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook-common all 2.4.1-1 [712 kB]
Get:18 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-markupsafe amd64 0.23-2build2 [15,5 kB]
Get:19 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-jinja2 all 2.8-1 [109 kB]
Get:20 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-pycurl amd64 7.43.0-1ubuntu1 [43,3 kB]
Get:21 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tornado amd64 4.2.1-1ubuntu3 [273 kB]
Get:22 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-zmq amd64 15.2.0-0ubuntu4 [200 kB]
Get:23 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ipython-notebook all 2.4.1-1 [48,4 kB]
Get:24 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 isympy all 0.7.6.1-1 [82,5 kB]
Get:25 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libaec0 amd64 0.3.2-1 [18,0 kB]
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Get:31 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-antlr all 2.7.7+dfsg-6ubuntu1 [19,0 kB]
Get:32 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-bs4 all 4.4.1-1 [64,2 kB]
Get:33 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-chardet all 2.3.0-2 [96,3 kB]
Get:34 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 libdsdp-5.8gf amd64 5.8-9.1ubuntu2 [192 kB]
Get:35 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cvxopt amd64 1.1.4-1.4 [1.344 kB]
Get:36 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-cycler all 0.9.0-1 [5.426 B]
Get:37 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-dateutil all 2.4.2-1 [42,5 kB]
Get:38 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-glade2 amd64 2.24.0-4ubuntu1 [9.078 B]
Get:39 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-gmpy amd64 1.17-1 [91,1 kB]
Get:40 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-html5lib all 0.999-4 [83,1 kB]
Get:41 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pil amd64 3.1.2-0ubuntu1.1 [312 kB]
Get:42 http://be.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 python-imaging all 3.1.2-0ubuntu1.1 [4.596 B]
Get:43 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-jdcal all 1.0-1build1 [7.702 B]
Get:44 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-joblib all 0.9.4-1 [74,6 kB]
Get:45 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-lxml amd64 3.5.0-1build1 [819 kB]
Get:46 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB]
Get:47 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib-data all 1.5.1-1ubuntu1 [2.414 kB]
Get:48 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-pyparsing all 2.0.3+dfsg1-1ubuntu0.1 [35,4 kB]
Get:49 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-tz all 2014.10~dfsg1-0ubuntu2 [31,5 kB]
Get:50 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-numpy amd64 1:1.11.0-1ubuntu1 [1.763 kB]
Get:51 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-matplotlib amd64 1.5.1-1ubuntu1 [3.888 kB]
Get:52 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-mpmath all 0.19-3 [387 kB]
Get:53 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-nose all 1.3.7-1 [116 kB]
Get:54 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-numexpr amd64 2.4.3-1ubuntu1 [129 kB]
Get:55 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-openpyxl all 2.3.0-1 [193 kB]
Get:56 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas-lib amd64 0.17.1-3ubuntu2 [1.538 kB]
Get:57 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pandas all 0.17.1-3ubuntu2 [2.386 kB]
Get:58 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-patsy all 0.4.1-2 [169 kB]
Get:59 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-py all 1.4.31-1 [62,5 kB]
Get:60 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pyglet all 1.1.4.dfsg-3 [726 kB]
Get:61 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-pytest all 2.8.7-4 [119 kB]
Get:62 http://be.archive.ubuntu.com/ubuntu xenial/main amd64 python-simplejson amd64 3.8.1-1ubuntu2 [60,4 kB]
Get:63 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy all 0.7.6.1-1 [2.252 kB]
Get:64 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-sympy-doc all 0.7.6.1-1 [4.774 kB]
Get:65 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-lib amd64 3.2.2-2 [353 kB]
Get:66 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables-data all 3.2.2-2 [45,3 kB]
Get:67 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-tables all 3.2.2-2 [335 kB]
Get:68 http://be.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-tk amd64 2.7.12-1~16.04 [26,3 kB]
Get:69 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlrd all 0.9.4-1 [107 kB]
Get:70 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-xlwt all 0.7.5+debian1-1 [83,5 kB]
Get:71 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-scipy amd64 0.17.0-1 [8.733 kB]
Get:72 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels-lib amd64 0.6.1-4 [173 kB]
Get:73 http://be.archive.ubuntu.com/ubuntu xenial/universe amd64 python-statsmodels all 0.6.1-4 [2.581 kB]
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Setting up libhdf5-10:amd64 (1.8.16+docs-4ubuntu1) ...
Setting up python-antlr (2.7.7+dfsg-6ubuntu1) ...
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Processing triggers for libc-bin (2.23-0ubuntu10) ...
➜ redundans git:(master) ✗ python2 redundans.py -v -i test/*_?.fq.gz -f test/contigs.fa -o test/run1
Options: Namespace(fasta='test/contigs.fa', fastq=['test/5000_1.fq.gz', 'test/5000_2.fq.gz', 'test/600_1.fq.gz', 'test/600_2.fq.gz'], identity=0.51, iters=2, joins=5, limit=0.2, linkratio=0.7, log=', mode 'w' at 0x7f85d1de31e0>, longreads=[], mapq=10, mem=16, minLength=200, nocleaning=True, nogapclosing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.8, reference='', resume=False, threads=4, tmp='/tmp', usebwa=False, verbose=True)

##################################################
[Mon May 7 11:29:18 2018] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80

##################################################
[Mon May 7 11:29:29 2018] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0
test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0

##################################################
[Mon May 7 11:29:29 2018] Scaffolding...
iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].
1526 pairs. 558 in different contigs [36.57%].
iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].
1077 pairs. 124 in different contigs [11.51%].
iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].
3417 pairs. 396 in different contigs [11.59%].
iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].
3398 pairs. 0 in different contigs [0.00%].

##################################################
[Mon May 7 11:29:34 2018] Gap closing...
iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133

##################################################
[Mon May 7 11:29:35 2018] Final reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
[WARNING] Nothing reduced!
test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00

##################################################
[Mon May 7 11:29:35 2018] Reporting statistics...
#fname contigs bases GC [%] contigs >1kb bases in contigs >1kb N50 N90 Ns longest
test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390

##################################################
[Mon May 7 11:29:35 2018] Cleaning-up...
#Time elapsed: 0:00:17.376924

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Rahul Nayak — Fri, 11 May 2018 05:07:45 -0500

MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 times faster than the current PBcR-Mhap pipeline. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON.

https://www.nature.com/articles/nmeth.4432

Address of the bookmark: https://github.com/xiaochuanle/MECAT

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Fri, 24 Jan 2020 06:04:40 -0600

gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

Tools for RNA classification

Abhi — Tue, 08 Nov 2022 03:39:11 -0600

barrnap - https://github.com/tseemann/barrnap

CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server)

CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server)

Infernal - http://eddylab.org/infernal/, https://github.com/EddyRivasLab/infernal

NCBI RefSeq - https://www.ncbi.nlm.nih.gov/refseq/

Rfam - http://rfam.xfam.org/, https://docs.rfam.org/en/latest/index.html

SILVA - https://www.arb-silva.de/

RNAmmer - http://www.cbs.dtu.dk/services/RNAmmer/ (web server, standalone download link)

Bioinformatics Tools for Phylogeny !

BioStar — Mon, 06 Nov 2023 03:09:59 -0600

Direct access to the individual tools available on this server.

Multiple Alignment:	Phylogeny:	Tree viewers:	Utilities:
MUSCLE	PhyML	TreeDyn	Gblocks
T-Coffee / 3DCoffee	TNT	Drawgram	Jalview
ClustalW	BioNJ	Drawtree	Readseq
ProbCons	MrBayes	ATV (A Tree Viewer)	Built-in converter