nylander/fastagap

Stars
2
Language
Perl
License
MIT License
Created over 4 years ago
Updated about 1 year ago

nylander/fastagap

nylander

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Remove or replace gaps in fasta formatted files

catfasta2phyml

Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

MrModeltest2

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 formats

grepfasta

Yet another grep for FASTA formatted files - with regexp capacity!

get_fasta_info

Some useful summary tools for FASTA formatted files

plotMCMCoutput

Shell scripts (bash) for plotting MCMC output (e.g., from MrBayes v.3, BEAST, etc) using gnuplot

reorient_fasta

Reverse-complement DNA sequences as needed in relation to a reference. Based on blastn.

Check_MD5SUMS

Check md5 sums for all .md5 and MD5SUMS files found in directory tree

ptemplate

ptemplate -- A project template

saturation.plot

Code for for displaying the relationship between the uncorrected (P-) distance and the distance on a phylogenetic tree

MrAIC

Perl script for selecting DNA substitution models using PhyML

consensus-sequence

FastEAR

FastEAR - Fast(er) Extraction of Alignment Regions from FASTA

fastp-cleaning

Clean fastq files with fastp

taxid2scientific_name

Get scientific name from Genbank taxon ID - or the other way around

phy2fas

Phylip to fasta converter using BioPerl

Align-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 fasta

Easy_webshare_on_UPPMAX

Easy file sharing on UPPMAX

DIVA-Dispersal-Vicariance-Analysis

Downloaded from SourceForge

pMrAIC

run-mrbayes-on-uppmax

Notes on running MrBayes on UPPMAX compute resources