SethMusker

lavaan

an R package for structural equation modeling and more

misa

mixed sample analysis

App-SpaM

Alignment-free Phylogenetic Placement using filtered SPAced word Matches

report

:scroll: :tada: Automated reporting of objects in R

phlash

Accelerated Bayesian inference of population size history from whole genome data.

Variant-Calling

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

computerraria

A fully compliant RISC-V computer made inside the game Terraria

dadi-cli

Automated and distributed population genetic model inference from allele frequency spectra

Orion

A machine learning library for detecting anomalies in signals.

PersonalUtilities

spruceup

:christmas_tree: spruceup

Captus

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

diCal2

diCal2 infers complex demographic histories from whole-genome sequencing data

dynamicviz

PyPythia

Lightweight python library for predicting the difficulty of alignments in phylogenetics

HybPiper

Recovering genes from targeted sequence capture data

ASTER

Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)

HerbChomper

A bioinformatic tool for trimming poorly-aligned ends from DNA sequences

manuscript-templates

LaTeX templates for manuscripts. bioRxiv preprint and journal submission templates. For use on Overleaf.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

phyutility

Start_repos

Some tips for noobs on getting started with version control.

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

NetRAX

Phylogenetic Network Inference without ILS

wQFM-2020

wQFM implementation in Java

ParalogWizard

QCF

Quartet concordance factor estimation

phyloscripts

Helper scripts for processing and visualization of phylogenetics datasets

admixtools