Pinned Repositories
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.
HBinspector
Script to produce the hidden break plot from a 28S sequence and a paired RNA-seq dataset
LBRem
A script to remove long branches from a phylogenetic tree
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.
PACtool
This is a project on GWAS using Python
ParaFilter
phy2nexus
Converts a PHYLIP alignment to interleaved NEXUS alignment, using the PAUP* software
PorthoMCL-parser
StrangeOrthoFilter
A script to filter out orthogroups that are unsuitable for downstream analyses.
pnatsi's Repositories
pnatsi/OGFilter
A script that parses the OrthoFinder output and keeps only the orthogroups that meet specific criteria
pnatsi/orthocounts2bin
A script to get from Orthogroups.GeneCount.tsv to a gene presence/absence binary alignment.
pnatsi/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.
pnatsi/PACtool
This is a project on GWAS using Python
pnatsi/HBinspector
Script to produce the hidden break plot from a 28S sequence and a paired RNA-seq dataset
pnatsi/ParaFilter
pnatsi/LBRem
A script to remove long branches from a phylogenetic tree
pnatsi/phy2nexus
Converts a PHYLIP alignment to interleaved NEXUS alignment, using the PAUP* software
pnatsi/PorthoMCL-parser
pnatsi/StrangeOrthoFilter
A script to filter out orthogroups that are unsuitable for downstream analyses.
pnatsi/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.
pnatsi/hiddenbreak
Scripts related to the 28S rRNA hidden break analysis
pnatsi/MonoDeutData
Data for paper examining support for monophyly of Deuterostomia
pnatsi/orthosims
pnatsi/pnatsi.github.io
pnatsi/Reading-PCA
pnatsi/Seq-Gen
Sequence simulator
pnatsi/Sparidae_2019
Scripts used in Natsidis et al (2019)
pnatsi/StarSeeker