Alternatives and similar repositories for p4-phylogenetics

Users that are interested in p4-phylogenetics are comparing it to the libraries listed below

• BenoitMorel / ParGenes
  A massively parallel tool for model selection and tree inference on thousands of genes
  ☆50Updated last year
• clwgg / nQuire
  A statistical framework for ploidy estimation using NGS short-read data
  ☆60Updated 7 years ago
• blaxterlab / blobology
  Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …
  ☆47Updated 3 years ago
• sjspielman / phyphy
  Python HyPhy: Facilitating HyPhy execution and parsing
  ☆21Updated 3 years ago
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆32Updated 3 years ago
• MaoYafei / TREEasy
  A tool to infer species tree and phylogenetic network from multilocus data
  ☆32Updated 5 years ago
• GATB / gatb-minia-pipeline
  GATB Minia assembly pipeline
  ☆30Updated 2 years ago
• mrmckain / Fast-Plast
  Automated de novo assembly of whole chloroplast genomes.
  ☆47Updated 11 months ago
• ballesterus / UPhO
  Scripts for homology and orthology assessment from genomic sequences.
  ☆19Updated 4 years ago
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆68Updated 7 years ago
• fethalen / Patchwork
  Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
  ☆36Updated last year
• davidemms / STAG
  STAG: Species Tree from All Genes
  ☆34Updated 6 years ago
• ranwez / MACSE_V2_PIPELINES
  This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MA…
  ☆34Updated 2 years ago
• cboursnell / crb-blast
  Conditional Reciprocal Best Blast
  ☆41Updated 8 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• JLSteenwyk / PhyKIT
  a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
  ☆74Updated 3 weeks ago
• lutteropp / QuartetScores
  Code for computing various support scores for internodes
  ☆19Updated 5 years ago
• JosephCrispell / homoplasyFinder
  A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
  ☆20Updated 4 years ago
• rderelle / Broccoli
  orthology assignment using phylogenetic and network analyses
  ☆45Updated 5 months ago
• marekborowiec / spruceup
  spruceup
  ☆25Updated 2 weeks ago
• rbouckaert / DensiTree
  Automatically exported from code.google.com/p/densitree
  ☆28Updated last month
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated 3 weeks ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• shahab-sarmashghi / Skmer
  Fast and accurate tool for estimating genomic distances between genome-skims
  ☆45Updated last year
• dportik / SuperCRUNCH
  A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local seq…
  ☆41Updated last year
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• katholt / RedDog
  ☆36Updated 3 years ago
• bioinf / Sibelia
  Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.
  ☆69Updated 4 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• combogenomics / medusa
  A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.
  ☆45Updated 4 years ago