ipyrad

Here are 4 public repositories matching this topic...

edgardomortiz / fineRADstructure-tools

Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

structure haplotypes stacks gbs radseq pyrad ipyrad fineradstructure

Updated Mar 24, 2020
Python

edgardomortiz / paralog-finder

Star

Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)

rad gbs radseq paralog ipyrad

Updated Sep 4, 2019
Python

NIGMS / Population-Genomics-and-Phylogenetics-with-RADseq

Star

This repository provides a comprehensive tutorial for phylogenetic analysis, covering data collection, sequence alignment, tree construction, and interpretation. It runs on AWS SageMaker using Jupyter notebooks and includes tools like MAFFT, Nextclade, and IQ-TREE.

python bioinformatics gcp computational-biology phylogenetic-trees phylogenetics population-genetics high-throughput-sequencing genome-assembly r-programming radseq ipyrad ddrad-seq iqtree phylogenetic-inference

Updated Jun 6, 2025
Jupyter Notebook

camayal / alignment2hdf5

Star

A simple script to convert fasta and nexus alignments into HDF5 databases compatible with Superbpp, ipyrad and ipyrad analysis

converter ipyrad superbpp

Updated Oct 28, 2021
Python

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