<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35559?offset=30 https://bioinformaticsonline.com/bookmarks/view/41969/shadowcaster-a-hybrid-approach-for-the-detection-of-horizontal-gene-transfer-events-in-prokaryotes Tue, 14 Jul 2020 06:42:10 -0500 https://bioinformaticsonline.com/bookmarks/view/41969/shadowcaster-a-hybrid-approach-for-the-detection-of-horizontal-gene-transfer-events-in-prokaryotes <![CDATA[ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes]]> ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in prokaryotes.

https://www.mdpi.com/2073-4425/11/7/756/htm

https://shadowcaster.readthedocs.io/en/latest/

https://github.com/dani2s/ShadowCaster_testData

Address of the bookmark: https://github.com/dani2s/ShadowCaster

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40703/%CF%80-cyc-a-reference-free-snp-discovery-application-using-parallel-graph-search Tue, 28 Jan 2020 03:34:23 -0600 https://bioinformaticsonline.com/bookmarks/view/40703/%CF%80-cyc-a-reference-free-snp-discovery-application-using-parallel-graph-search <![CDATA[Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search]]> Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only

Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical for large error prone genomes which makes the assembly process produce an excessive number of false positive cycles.  Our solution is to search the graph in multicores shared memory parallel mode using graph decomposition then use filtering method to generate good quality SNPs.

https://arxiv.org/abs/1809.06700

https://github.com/redayounsi/2KP2P

/2kp2omp/bin/main_2kp2_K63_C2 -i fastq_files.txt -o fungus_bub.fasta -r stat_fungus.txt -c cov_fungus_hash.txt -k 63 -h 20 -b 100 -g 600 -l 100 -f 16 -t 5.0 -x 1 -v 0 -p 1 -y 1 -u 1

 

Address of the bookmark: https://github.com/redayounsi/2KP2P

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38752/hgtector-an-automated-method-facilitating-genome-wide-discovery-of-putative-horizontal-gene-transfers Mon, 21 Jan 2019 06:50:05 -0600 https://bioinformaticsonline.com/bookmarks/view/38752/hgtector-an-automated-method-facilitating-genome-wide-discovery-of-putative-horizontal-gene-transfers <![CDATA[HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers]]> A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics

Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar (katharinad@gmail.com)

Affiliation: Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, USA

Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics. 2014. 15:717.

Usage: Simply execute perl HGTector.pl, or, open GUI.html in a web browser to see a step-by-step wizard.

Download HGTector 0.2.2.

Address of the bookmark: https://github.com/DittmarLab/HGTector

]]> Jit https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage Mon, 10 Feb 2014 05:57:29 -0600 https://bioinformaticsonline.com/pages/view/8265/list-of-generic-simulation-softwaretoolsresource-with-brief-description-and-homepage <![CDATA[List of generic simulation software/tools/resource with brief description and homepage !!!]]> List of generic simulation software/tools/resource with brief description and homepage

image

ALF
A Simulation Framework for Genome Evolution
http://www.cbrg.ethz.ch/alf

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

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
http://www.wyomingbioinformatics.org/liberlesgroup/cass/

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

CoalFace
CoalFace is a simulation of the coalescent process with the visual display of gene genealogies.
http://web.up.ac.za/default.asp?ipkcategoryid=3283

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.html

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/page36926_fr.html

EggLib
EggLib is a C++/Python library and program package for evolutionary genetics and genomics.
http://egglib.sourceforge.net/

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
http://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://flux.sammeth.net/simulator.html

ForSim
ForSim: A Forward Evolutionary Computer Simulation
http://www.anthro.psu.edu/weiss_lab/research.shtml

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
http://genfaculty.rutgers.edu/hey/software#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/download/fregen/documentation_html.html

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/

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.
http://webs.uvigo.es/acraaj/genomepop2.htm

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/

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/

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.php

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/

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://bit.ly/rlsim-git

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://linum.cofc.edu/software.html#metasim

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/

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/

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://www.chg.duke.edu/research/simla.html

SimPed
A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures
http://www.hgsc.bcm.tmc.edu/content/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/simucomplexdisease

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/

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/

Vortex
VORTEX is an individual-based simulation model for population viability analysis (PVA).
http://www.vortex9.org/vortex.html

References:

Image www.evolution-of-life.com

www.cancer.gov

]]> Jit https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources Tue, 28 Jun 2022 04:08:06 -0500 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources <![CDATA[List of comparative genomics resources !]]>

Compare structural and functional annotations of proteins between sequenced genomes.

View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.

Find information about orthologous genes in prokaryotes.

Search for publicly available QTL data on livestocks and animal species.

Find information about bovine genomics data.

A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.

A database resource of developmentally associated conserved non-coding elements.

Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.

Find coexpressed gene lists and networks in human and mouse.

Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.

A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.

Find information about the ancestral relationship between genes.

Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.

Conduct comparative biometric analysis of chromosomes of different organisms.

Search for Indices of gene and transcripts in human and mouse.

Search and compare 12 new and old Drosophila genomes.

Access to whole genome alignments of human, mouse, rat and fish sequences.

Find eukaryotic paralog/paralogon information.

Analyze the evolutionary process of overlapping genes when comparing different species.

The first publicly available system reported to handle inter-species gene mention normalization.

A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.

Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.

Find information about mutated mouse genes.

A data management and analysis system for metagenomes

Search for influenza sequence, vaccine, and drug resistance information.

LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.

The missing link between multi-species full genome comparisons and functional analysis.

Conduct comparative analysis of completely sequenced microbial genomes.

A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.

Find information about 1000s of microbial genomes.

A database dedicated to the study of genome conservation.

Explore orthologous relations across 352 complete genomes.

Browse complete genomes in several clades.

A database of orthologous genomic markers for placental mammal phylogenetics.

Conduct genome wide functional and structural analysis.

Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.

Compare phenotypes of a given gene or gene set in different model organisms.

Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.

Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.

Search for genomic information on nematode satellite species Pristionchus pacificus.

Find information about related protein sequences.

Database hosting genomics and post-genomics data from multiple protozoans.

A database of pseudogene families based on the protein families from the Pfam database.

Find genomic information about mammals.

Find information about predicted regulons in prokaryotic transcription regulation.

Perform systematic comparison of proteome data among species.

A comparative map viewer dedicated to the biology of the Solanaceae family.

Analyze data from functional analysis on fragmented microbial genetic material.

Visualize and explore comparative genomic hybridization data sets.

Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.

Search for information on adaptive evolution in gene families of higher plants and chordate.

Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.

Conduct a comprehensive analysis of genes and genomes.

An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources

Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.

Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)

A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/35800/scikit-bio%E2%84%A2-is-an-open-source-bsd-licensed-python-package-providing-data-structures-algorithms-and-educational-resources-for-bioinformatics Fri, 02 Mar 2018 04:29:47 -0600 https://bioinformaticsonline.com/bookmarks/view/35800/scikit-bio%E2%84%A2-is-an-open-source-bsd-licensed-python-package-providing-data-structures-algorithms-and-educational-resources-for-bioinformatics <![CDATA[scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.]]> scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.

Address of the bookmark: http://scikit-bio.org/

]]> Jit https://bioinformaticsonline.com/blog/view/43898/online-resources-on-must-read-papers-in-evolutionary-biology-for-a-literature-club Tue, 28 Jun 2022 07:29:08 -0500 https://bioinformaticsonline.com/blog/view/43898/online-resources-on-must-read-papers-in-evolutionary-biology-for-a-literature-club <![CDATA[Online resources on must-read papers in evolutionary biology, for a literature club]]> 1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J. A., Goldstein, D. B., & Patel, N. H. (2007). Evolution. Cold Spring Harbor Laboratory Press. - Papers from a course named "Classics in Evolutionary Biology": Evolutionary Synthesis 1. Haldane, J. B. S. 1932. The causes of evolution. Longmans. New York. (esp. Ch. IV). 2. Fisher, R. A. 1930. The genetical theory of natural selection. Oxford University Press, Oxford. Selected Sections - Fundamental Theorem. Genetic Variation 1a. Lewontin, R. C., and J. L. Hubby. 1966. A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics. 54:595-609. 1b. Sachidandam et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. 409: 928-33. 2. Wright S., Dobzhansky T., Hovanitz W. 1942 Genetics of natural populations VII The allelism of lethals in the third chromosome of Drosophila pseudoobscura. Genetics 27: 363-394. Recombination and evolution 1. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits to artificial selection. Genet. Res. 8:269-294. 2. Maynard Smith and Haigh. 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35. Understanding sequence variation 1. Begun D. J., Aquadro C. F., 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rate in Drosophila melanogaster. Nature 356: 519-520. 2. Green R. E., Reich D., Pääbo S., 2010 A draft sequence of the Neandertal genome. Science 328: 710-722. Quantitative Genetics: variation in complex traits 1. Galton F., 1877 Typical laws of heredity. Nature 15: 492-495- 512-514- 532-533. 2. Turelli M., 1984 Heritable genetic variation via mutation-selection balance: Lerch's Zeta meets the abdominal bristle. Theor. Popul. Biol. 25: 138-193. Quantitative Genetics: finding the genes 1. Shrimpton A. E., Robertson A., 1988 The Isolation of polygenic factors controlling bristle score in Drosophila melanogaster II Distribution of third chromosome bristle effects within chromosome sections. Genetics 118: 445-459. 2. Boyle E. A., Li Y. I., Pritchard J. K., 2017 An expanded view of complex traits: from polygenic to omnigenic. Cell 169: 1177-1186. Neutral Evolution 1. Kimura, M. 1968. Evolutionary rate at the molecular level. Science. 217:624-626. 2a. Kern A. D., Hahn M. W., 2018 The Neutral Theory in Light of Natural Selection. Molecular Biology and Evolution 110: 21077-6. 2b. Jensen J. D., Payseur B. A., Stephan W., Aquadro C. F., Lynch M., Charlesworth D., Charlesworth B., 2018 The importance of the Neutral Theory in 1968 and 50 years on: a response to Kern and Hahn 2018. Evolution 112: 2109-4. 2c. Ellegren & Galtier. 2016. Determinants of genetic diversity. Nature Reviews Genetics. Mutation and Genetic Variability 1. Luria, S. E., and M. Delbrück. 1943. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics. 28(6):491-511. 2. Hill, W G. 1982. "Rates of Change in Quantitative Traits From Fixation of New Mutations." Proceedings of the National Academy of Sciences (U.S.A.) 79: 142-45. Testing for selection 1. McDonald & Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 2. Begun, et al. Mol. Biol. Evol. 16, 1816-1819 (1999). 3. Siddiq et al. 2016. Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nature Ecology & Evolution. The shifting balance 1. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the VI International Congress of Genetics: 1. pp 356-366. 2. Coyne, J.A., N.H. Barton, and M. Turelli. 1997. A critique of Wright's shifting balance theory of evolution. Evolution 51: 643-671. 3. Barton. 2016. Sewall Wright on Evolution in Mendelian Populations and the "Shifting Balance". Genetics. Evolution of Sex 1. Muller, H.J. 1964. The relation of recombination to mutational advance. Mutation Res. 1(1):2-9 2. McDonald et al. 2016. Sex speeds adaptation by altering the dynamics of molecular evolution. Nature. Kin Selection, Cooperation, and Conflict 1. Hamilton, W. D. 1964. The genetical evolution of social behaviour I. Journal of Theoretical Biology. 7:1-52. 2. Trivers, R. L. 1974 Parent-offspring conflict. American Zoologist. 14(1):249-264. Sexual Selection 1. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor. Biol. 53:205-214. 2. Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating preferences and the paradox of the lek. Nature. 350:33-38. Fitness Landscapes 1. Dean, A. 1995. A Molecular Investigation of Genotype by Environment Interactions. Genetics. 139:19-33. 2. Costanzo et al. 2010. The Genetic Landscape of a Cell. Science. Speciation 1. Coyne, J. A., and H. A. Orr. 1989. Patterns of speciation in Drosophila. Evolution. 43:362-381. 2. Corbett-Detig et al. 2013. Genetic incompatibilities are widespread within species. Nature. 2. *Marcos Antezana:* Valen, L. v. 1975. Energy and Evolution. University of Chicago, Department of Biology. 3. *Remco Folkertsma:* 1. The work by Hopi Hoekstra on local adaptation and oldfield mice 2. Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller, I., ... & Wolf, J. B. (2014). The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science, 344(6190), 1410-1414. 4. *Joshka Kaufmann and Leslie Turner* They offer us a link to 'papers every evolutionary biologist should read', the papers are collected by Leslie Turner. https://static1.squarespace.com/static/53e8cb7ce4b02c4bc3aeeee4/t/5ab8fcb670a6ad55c67fcdf4/1522072758665/EvoBioClassicsRefList.pdf 5. *Sarah Stockwell* Matt Ridley collected classic papers in evolutionary biology and printed part of these papers in his book Evolution (see Matt Ridley. Evolution (Univ. of Oxford Press, 2nd edition, 2004))]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/39830/the-extensive-de-novo-te-annotator-edta Thu, 08 Aug 2019 04:05:36 -0500 https://bioinformaticsonline.com/bookmarks/view/39830/the-extensive-de-novo-te-annotator-edta <![CDATA[The Extensive de novo TE Annotator (EDTA)]]> The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.

Address of the bookmark: https://github.com/oushujun/EDTA

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/42271/mcclintock-meta-pipeline-to-identify-transposable-element-insertions-using-next-generation-sequencing-data Tue, 27 Oct 2020 00:21:18 -0500 https://bioinformaticsonline.com/bookmarks/view/42271/mcclintock-meta-pipeline-to-identify-transposable-element-insertions-using-next-generation-sequencing-data <![CDATA[McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data]]> an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae. 

Address of the bookmark: https://github.com/bergmanlab/mcclintock

]]> BioStar https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals Tue, 25 Apr 2017 05:03:27 -0500 https://bioinformaticsonline.com/blog/view/32358/list-of-goi-approved-peer-reviewed-bioinformatics-and-computational-biology-journals <![CDATA[List of GOI approved peer reviewed bioinformatics and computational biology journals]]> Unfortunately, we now live in a world where the integrity of peer-reviewed journals is being threatened by the rise of the academic version of fake news – something many call “predatory publishing".  Mostly in academic publishing world, "predatory open access publishing" is an exploitative open-access publishing business model that involves charging publication fees to authors without providing the editorial and publishing services associated with legitimate journals (open access or not).

Nearly 20% of the such journals have a flashy impact factor and quick publication time, which are quick give-aways. Interestingly, under contact address, some journal websites do not even provide any address to contact. All of this has led to the emergence of a new and dark market of deceptive publishers that exploit the concept of open access and provide channels for “scientific journal” publication with little or no peer review. For a fee, they will publish almost anything – even if the study was fatally flawed. And these journals provide a forum that can be used as a channel to publish fraudulent “advocacy research.” You can find list of certain such publishers at "Beall's List" http://beallslist.weebly.com/

Keeping all these in mind, Government of India (GOI) decided to approved certain bioinformatics and computational biology journals for your research publication.

Following are the list of GOI validated and peer reviewed bioinformatics and computational biology journals:

NOTE:Each journal details are in following order Tittle\nSource\nSubject.
Point to remember: The list of journals are NOT sorted in any ascending or descending order.

If I missed any other GOI validated bioinformatics journal, then please report me in comment section.

Open Bioinformatics Journal
Scopus
Computer Science; Engineering; Medicine

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
WoS
BIOLOGY & BIOCHEMISTRY

Advances and Applications in Bioinformatics and Chemistry
Scopus
Biochemistry, Genetics and Molecular Biology Chemistry; Computer Science

Advances in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Engineering

Applied Bioinformatics
Scopus
Agricultural and Biological Sciences; Computer Science

BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Bioinformatics and Biology Insights
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics

BMC BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

BRIEFINGS IN BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
Scopus
Medicine

Current Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Current Protocols in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology

JOURNAL OF COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS
ICI
BIOLOGICAL SCIENCE

Journal of integrative bioinformatics
Scopus
Medicine

Journal of Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Mathematical Biology and Bioinformatics
Scopus
Engineering; Mathematics

Trends in Bioinfprmatics
Scopus
Computer Science

Eurasip Journal on Bioinformatics and Systems Biology
Scopus
General; Computer Science; Mathematics; Medicine

Evolutionary Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Genomics, Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE-ACM Transactions on Computational Biology and Bioinformatics
WoS
COMPUTER SCIENCE

International Journal of Bioinformatics Research and Application
Scopus
Biochemistry, Genetics and Molecular Biology; Medicine, Health

International Journal o f Data M ining and Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

IPSJ Transactions on Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Computer Science

Journal of Bioinformatics and Computational Biology
WoS & Scopus
COMPUTER SCIENCE

Journal of Clinical Bioinformatics
Scopus
Medicine

PLoS Computational Biology
WoS & Scopus
BIOLOGY & BIOCHEMISTRY

Reviews in Computational Chemistry
WoS & Scopus
CHEMISTRY

RSC Theoretical and Computational Chemistry Series
Scopus
Chemistry; Computer Science

Annual Reports in Computational Chemistry
Scopus
Chemistry; Mathematics

Computational and Structural Biotechnology Journal
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Computational and Theoretical Chemistry
WoS & Scopus
CHEMISTRY

COMPUTATIONAL BIOLOGY AND CHEMISTRY
WoS & Scopus
COMPUTER SCIENCE

COMPUTATIONAL CHEMISTRY
WoS
CHEMISTRY

Journal of Theoretical and Computational Chemistry
Scopus
Chemistry; Computer Science

Theoretical and Computational Chemistry
Scopus
Chemistry

Wiley Interdisciplinary Reviews: Computational Molecular Science
Scopus
Biochemistry, Genetics and Molecular Biology;Chemistry; Computer Science; Materials Science; Mathematics

Wiley Interdisciplinary Reviews- Computational Molecular Science
WoS
CHEMISTRY

Interdisciplinary sciences, computational life sciences
Scopus
Medicine

Interdisciplinary Sciences-Computational Life Science
WoS
Biology and Biochemistry

International Journal of Computational Biology and Drug Design
Scopus
Computer Science; Pharmacology, Toxicology and Pharmaceutics

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