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https://github.com/amkozlov/raxml-ng
Software phylogenetic tree inference tool which uses maximum likelihood optimality criterion. Used for maximum likelihood phylogenetic inference. Offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML.
Proper citation: RAxML Next Generation (RRID:SCR_022066) Copy
A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.
Proper citation: vcflib (RRID:SCR_001231) Copy
http://crab.rutgers.edu/~dslun/csdeconv/index.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.
Proper citation: CSDeconv (RRID:SCR_000016) Copy
http://www.mattmahoney.net/dc/fastqz/
Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output.
Proper citation: fastqz (RRID:SCR_001006) Copy
http://hihg.med.miami.edu/software-download/seqem-version-1.0
Online tool for utilizing a genotype calling algorithm for next-generation sequence data.
Proper citation: SeqEM (RRID:SCR_002021) Copy
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Proper citation: ImageJ (RRID:SCR_003070) Copy
http://www-stat.stanford.edu/~tibs/SAM/
Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.
Proper citation: SAM (RRID:SCR_010951) Copy
http://bioen-compbio.bioen.illinois.edu/FusionHunter/
Software for identifying fusion transcripts using paired-end RNA-seq.
Proper citation: FusionHunter (RRID:SCR_011895) Copy
https://gitlab.com/kyrgyzov/lsa_slurm
Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics.
Proper citation: lsa_slurm (RRID:SCR_018134) Copy
https://github.com/Pithikos/C-Thread-Pool
Software for minimal but powerful thread pool in ANSI C.
Proper citation: C Thread Pool (RRID:SCR_023999) Copy
https://github.com/smirarab/sepp/
Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.
Proper citation: sepp (RRID:SCR_024327) Copy
https://www.teuniz.net/edflib/
Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.
Proper citation: EDFlib (RRID:SCR_024010) Copy
http://www.dclunie.com/dicom3tools.html
Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.
Proper citation: Dicom3tools (RRID:SCR_024008) Copy
https://github.com/stamatak/AxPcoords.dist
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.
Proper citation: AxPcoords (RRID:SCR_023971) Copy
http://sco.h-its.org/exelixis/web/software/AxParafit/index.html
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.
Proper citation: AxParafit (RRID:SCR_023968) Copy
https://github.com/nextstrain/auspice
Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.
Proper citation: Auspice (RRID:SCR_023966) Copy
https://github.com/sanger-pathogens/assembly-stats
Software to get assembly statistics from FASTA and FASTQ files.
Proper citation: assembly-stats (RRID:SCR_023963) Copy
https://github.com/thegenemyers/DEXTRACTOR
Software as Bax file decoder and data compressor.
Proper citation: DEXTRACTOR (RRID:SCR_024005) Copy
https://github.com/nexml/nexml.java
Software repository contains java code for NeXML processing.
Proper citation: Java NeXML libraries and tools (RRID:SCR_024084) Copy
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