nylander/plotMCMCoutput

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Language OpenEdge ABL
License
MIT License
Created almost 11 years ago
Updated over 1 year ago

nylander/plotMCMCoutput

nylander

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

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

reorient_fasta

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

fastagap

Remove or replace gaps in fasta formatted files

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