BOL: Related items

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs

Surabhi Chaudhary — Sat, 25 Dec 2021 00:13:31 -0600

VCF2PopTree is a client-side software written in Javascript and it runs purely within the user’s computer/browser. VCF2PopTree is compatible with all population browsers including Chrome, Opera, Edge and Firefox and works equally efficient in Mac, Windows and Linux (Ubuntu).

Furthermore, it displays the tree in a mobile phone (iPhone and Android) if the input file size is small. CITATION: Subramanian, S., Ramasamy, U. and Chen, D. (2019). VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs. Peer J. x:yy.

Address of the bookmark: https://github.com/sansubs/vcf2pop

dna2bit: an ultra-fast and accurate genomic distance estimation software

Neel — Wed, 13 Aug 2025 19:56:21 -0500

dna2bit: an ultra-fast and accurate genomic distance estimation software

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation.

Address of the bookmark: https://github.com/lijuzeng/dna2bit

Seal: SEquence ALignment evaluation suite

Jit — Wed, 03 Jan 2018 05:05:46 -0600

Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

Reading a pre-existing reference genome from one or more FASTA files.
Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
Applying alignment tools to the genome and the reads through a standardized interface.
Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

Bowtie
BWA
MAQ
mrFAST
mrsFAST
Novoalign
SHRiMP
SOAPv2

Address of the bookmark: http://compbio.case.edu/seal/

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Abhi — Wed, 06 Oct 2021 07:01:14 -0500

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing

BioStar — Fri, 22 Dec 2017 00:31:06 -0600

AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity

The program with a detailed manual is available at https://sourceforge.net/projects/airvf/

Address of the bookmark: https://sourceforge.net/projects/airvf/

Orione – a web-based framework for NGS analysis in microbiology

Martin Jones — Wed, 23 Jul 2014 06:43:03 -0500

End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult due to a lack of interoperability, reproducibility, and transparency. To overcome these limitations researchers at CRS4, Italy have developed Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for NGS microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.

Reference

Cuccuru G1, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, Fotia G. (2014) Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics [Epub ahead of print]. [article]

Address of the bookmark: http://orione.crs4.it/

PhyloGrapher - Graph Visualization Tool

Jitendra Prajapati — Wed, 06 Apr 2016 19:06:48 -0500

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements).PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements.

More at http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

Blobsplorer

Jit — Tue, 14 Jun 2016 10:28:58 -0500

Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for collections of contigs with a view to separating out those belonging to different taxa.

Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html

I-PV: Interactive Protein Sequence Visualization

Jit — Mon, 03 Jul 2017 07:52:51 -0500

I-PV is a interactive data visualization software designed for inspection of protein sequences and mutation information. It is mainly used for Genetics and Bioinformatics. So what exactly makes it standout?

http://i-pv.org/ipv_rec

Address of the bookmark: http://i-pv.org/

sankeyNetwork with networkD3

Jit — Fri, 06 Apr 2018 12:07:55 -0500

You can also create Sankey diagrams with sankeyNetwork. Here is an example using downloaded JSON data:

https://en.wikipedia.org/wiki/Sankey_diagram

Address of the bookmark: https://christophergandrud.github.io/networkD3/#sankey