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alicut

A nice tool to cut out ALISCORE identified randomized sequence sections in multiple sequence alignments.

augustus

Genome annotation with AUGUSTUS

bacoca

BaCoCa (Base Composition Calculator) is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used for a detailed and statistical comprehensive data evaluation. Furthermore, the results can help to identify phylogenetic sequence biases which can lead to incorrect tree reconstructions. The program can handle hundreds of user specified gene and taxon partitions of a single sequence input file in one process run. BaCoCa is a command-line driven program written in PERL and works on WindowsPCs, Macs and Linux operating systems. Therefore, it can be easily integrated into automatic pipeline processes of phylogenomic studies.

beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees

beast2

Bayesian Evolutionary Analysis by Sampling Trees

biocode

Bioinformatics code libraries and scripts

bpp-phyl

Bio++ Phylogenetic Library

centroid-rna-package

Centroid RNA package

coevversioning

Coevolution

comap

A package for detecting coevolving positions in a sequence alignment, using COsubstitution MAPping.

dart

DNA, Amino Acid and RNA Tests

emboss

The European Molecular Biology Open Software Suite (clone of git://anonscm.debian.org/debian-med/emboss.git)

emboss-1

Unofficial mirror of the EMBOSS source

fasconcat

FASconCAT is a user-friendly software that concatenates rapidly different kinds of sequence data into one supermatrix file. Output files are either in FASTA, PHYLIP or NEXUS format and are directly loadable in phylogenetic programs like PAUP*, RAxML or MrBayes. FASconCAT can handle FASTA, PHYLIP and CLUSTAL formatted input files in one single run. It provides useful information about each input file and the concatenated supermatrix.

fasconcat-g

FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences. FASconCAT-G implemented process options can be invoked in any combination and performed during a single process run. FASconCAT-G can also read in and handle different file formats (FASTA, CLUSTAL, and PHYLIP) in a single run.

fastmg

fastmg-1

galaxy-rna-workbench

Galaxy RNA workbench

git

Git Source Code Mirror - This is a publish-only repository and all pull requests are ignored. Please follow Documentation/SubmittingPatches procedure for any of your improvements.

hmmer

HMMER: biological sequence analysis using profile HMMs

iqtree

IQ-TREE

iqtreegui

iqtreeGUI - A graphical user interface for IQ-TREE

learn-bioinformatics

messi

Modelling Evolution of Secondary Structure Interactions

mitobim

MITObim - mitochondrial baiting and iterative mapping

mitoseek

Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing

mitoz

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

mt_metazoan_models

Metazoan mitochondrial amino acid substitution models

nlopt

library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization

phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood