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alscores

A script that aligns fasta files using mafft and evaluates the alignments using Gblocks. It returns a score that indicates each alignment's quality based on Gblocks result.

f2pa

A script that runs OrthoFinder for a set of proteomes and produces gene presence/absence alignments in three possible formats (FASTA, PHYLIP, NEXUS). It can optionally run BUSCO analysis for the proteomes.

hbinspector

Script to produce the hidden break plot from a 28S sequence and a paired RNA-seq dataset

hiddenbreak

Scripts related to the 28S rRNA hidden break analysis

lbrem

A script to remove long branches from a phylogenetic tree

monodeutdata

Data for paper examining support for monophyly of Deuterostomia

ogfilter

A script that parses the OrthoFinder output and keeps only the orthogroups that meet specific criteria

orthocounts2bin

A script to get from Orthogroups.GeneCount.tsv to a gene presence/absence binary alignment.

orthosims

pactool

This is a project on GWAS using Python

parafilter

phy2nexus

Converts a PHYLIP alignment to interleaved NEXUS alignment, using the PAUP* software

pnatsi.github.io

porthomcl-parser

reading-pca

seq-gen

Sequence simulator

sparidae_2019

Scripts used in Natsidis et al (2019)

starseeker

strangeorthofilter

A script to filter out orthogroups that are unsuitable for downstream analyses.