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ptitle

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ptitle's starred repositories

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Language:Jupyter NotebookLicense:MITStargazers:223Issues:17Issues:142

scidataflow

Command line scientific data management tool

Language:RustLicense:MITStargazers:205Issues:3Issues:17

dggridR

Discrete Global Grids for R: Spatial Analysis Done Right

Language:C++License:AGPL-3.0Stargazers:160Issues:20Issues:64

veryfasttree

Efficient phylogenetic tree inference for massive taxonomic datasets

Language:C++License:NOASSERTIONStargazers:105Issues:13Issues:23

zoomerjoin

Superlatively-fast fuzzy-joins in R

Language:RLicense:GPL-3.0Stargazers:97Issues:6Issues:29

AMAS

Calculate summary statistics and manipulate multiple sequence alignments

Language:PythonLicense:NOASSERTIONStargazers:72Issues:7Issues:13

waywiser

Ergonomic tooling to assess models of spatial data

Language:RLicense:NOASSERTIONStargazers:38Issues:3Issues:20

ml-morph

Machine-learning-based morphometrics

Language:PythonLicense:GPL-3.0Stargazers:31Issues:3Issues:5

centerline

An R package to retrieve the centerline of polygons

Language:RLicense:NOASSERTIONStargazers:30Issues:2Issues:5

prequal

PREQUAL: a pre-alignment quality filter for comparative sequence analyses

Language:C++License:GPL-3.0Stargazers:30Issues:4Issues:4

bagels

open source bagel recipe; let's raise the quality of bagels worldwide :bagel: :rocket:

License:GPL-3.0Stargazers:26Issues:3Issues:3

chronumental

Estimating time trees from very large phylogenies

Language:PythonLicense:MITStargazers:24Issues:3Issues:15

phyloshapeR

Package to plot phylogenies with custom shapes

Language:RStargazers:22Issues:2Issues:0

phylomad

Language:RStargazers:19Issues:5Issues:10

coati

Codon-Aware Multiple Sequence Alignments

Language:C++License:MITStargazers:18Issues:4Issues:6

prepr

An R package to repair broken GIS polygons using the prepair (https://github.com/tudelft3d/prepair) Cpp library - mirror to the Gitlab repository..

Language:C++Stargazers:13Issues:4Issues:3

RISDM

R package to fit integrated SDM models (with PO, PA and abundance data)

Language:RLicense:LGPL-2.1Stargazers:12Issues:6Issues:2

SequenceBouncer

A Python3 script for removal of outlier sequences from a multiple sequence alignment (FASTA format).

Language:PythonLicense:GPL-3.0Stargazers:9Issues:2Issues:3

ecotrends

Spatio-temporal trends in habitat suitability from ecological niche models

Language:RLicense:NOASSERTIONStargazers:6Issues:0Issues:0

treepl

Repo to run treepl using bootstrap alignments

Language:PythonStargazers:6Issues:2Issues:2

LMdist

LMdist is an unsupervised algorithm for correcting oversaturated pairwise distance and dissimilarity measures. Compatible with any pairwise beta diversity measure, LMdist will uncover underlying environmental gradients and resolve arches/horseshoes in ordination.

Language:RLicense:AGPL-3.0Stargazers:5Issues:2Issues:0

DPAMSA

Language:PythonStargazers:5Issues:2Issues:2

ClockstaRX

Language:RStargazers:4Issues:0Issues:0

chronos

ultrametricity or bust

Language:RStargazers:4Issues:5Issues:3

utremi

Language:ShellLicense:GPL-3.0Stargazers:4Issues:3Issues:0

CASTLES

Coalescent-Aware Species Tree Length Estimation in Substitution-units

Language:MathematicaLicense:MITStargazers:4Issues:2Issues:2

PhyInformR

PhyInformR package

Language:RStargazers:2Issues:2Issues:1

biostats

Statistics app for introductory biology students

Language:RLicense:CC0-1.0Stargazers:1Issues:0Issues:0

how_we_work

Lab best practices and policies to conduct open, reproducible, and inspiring science that is efficient and fun

Stargazers:1Issues:0Issues:0

PKS-Test

The PKS Test software was designed to directly verify whether a phylogeny is clock-like following a Poisson law.

Language:TerraStargazers:1Issues:1Issues:0