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catfasta2phyml
Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted fileMrModeltest2
C program for selecting DNA substitution models using PAUP*Burntrees
Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)translate_fasta_headers
Translate long fasta headers to short - and back!beast2phy
Convert output trees from BEAST to other formatsgrepfasta
Yet another grep for FASTA formatted files - with regexp capacity!get_fasta_info
Some useful summary tools for FASTA formatted filesplotMCMCoutput
Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplotfastagap
Remove or replace gaps in fasta formatted filesCheck_MD5SUMS
Check md5 sums for all .md5 and MD5SUMS files found in directory treeptemplate
ptemplate -- A project templatesaturation.plot
Code for for displaying the relationship between the uncorrected (P-) distance and the distance on a phylogenetic treeMrAIC
Perl script for selecting DNA substitution models using PhyMLconsensus-sequence
FastEAR
FastEAR - Fast(er) Extraction of Alignment Regions from FASTAfastp-cleaning
Clean fastq files with fastptaxid2scientific_name
Get scientific name from Genbank taxon ID - or the other way aroundphy2fas
Phylip to fasta converter using BioPerlAlign-and-trees-parallel-workflow
Script for running a "standard" phylogenetic workflow on fasta-formatted input. In particular, parallel execution is done whenever possible.efasta2fasta
Convert extended fasta (efasta) to fastaEasy_webshare_on_UPPMAX
Easy file sharing on UPPMAXDIVA-Dispersal-Vicariance-Analysis
Downloaded from SourceForgepMrAIC
Parallel MrAICrun-mrbayes-on-uppmax
Notes on running MrBayes on UPPMAX compute resourcesLove Open Source and this site? Check out how you can help us