• Stars
    star
    2
  • Language
    Python
  • License
    GNU General Publi...
  • Created about 5 years ago
  • Updated 5 months ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

An accessible and flexible tool for fitting demographic models with moments using custom or published models (available here) and conducting goodness of fit tests.

More Repositories

1

dadi_pipeline

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.
Python
63
star
2

SuperCRUNCH

A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.
Python
41
star
3

LRSW-Taxonomic-Profiling-Tutorial

Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at the Jackson Laboratory.
13
star
4

Pandas-for-Population-Structure-Barplots

A jupyter notebook tutorial for making high-quality barplot figures from population structure analyses (Admixture, Structure) with Python & Pandas.
HTML
12
star
5

MonoPhylo

A python tool for rapidly assessing the monophyly of user-defined groups in phylogenetic trees.
Python
9
star
6

Stacks_pipeline

An automated workflow for processing ddRADseq data using Stacks v2.4. Starts with sequencer files, and ends with various input files for phylogenetic/phylogeography programs.
Python
9
star
7

Academic-CV-vs-Industry-Resume

A 1:1 comparison of my academic CV and industry resume, with some tips on making an industry resume.
7
star
8

TaxonomyAlign

Taxonomy-guided multiple sequence alignment for difficult genes, including 12S and 16S mitochondrial rRNA.
Python
4
star
9

admixture-wrapper

A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.
OpenEdge ABL
3
star
10

SSDi-Calculator

A Python tool for calculating sexual size dimorphism indices from body size data. Performs permutation tests to determine statistically significant sexual dimorphism.
Python
2
star
11

HiSSE_for_Afrobatrachia

Hidden state speciation and extinction analyses of sexual dichromatism in Afrobatrachian frogs.
R
2
star
12

Alignment_Refiner

A script to filter phylip alignments by minimum bp length, missing data across individual sequence or whole alignment, with subsequent trimming function to reduce missing data.
Python
2
star
13

Phylo_Wrapper_Scripts

Scripts to help automate various phylogenetic or phylogeography programs (Admixture, RAxML, CLUMPP + DISTRUCT). Also includes a script for replacing sample or taxon names in input files.
Python
2
star
14

Coverage_Calculator

Script to help calculate coverage of a sample or contigs within a sample for sequence capture data sets.
Python
1
star
15

Phylogenetic_Tree_Tools

Scripts for pruning taxa from tree files, performing Robinson-Foulds comparisons, and calculating node-support indices. All intended for a directory of tree files, rather than a single tree.
Python
1
star
16

Alignment_Assessment

A tool for summarizing and visualizing metrics for sequence alignment files in phylip format. Designed to execute on a directory containing up to several thousand phylip files.
Python
1
star
17

Convert-fasta-alignments-to-Structure-format

Convert a set of phased alignment fasta files into a Structure input file. Intended to work with seq-capture and ddRADseq datasets.
Python
1
star