Alternatives and similar repositories for PyPythia

Users that are interested in PyPythia are comparing it to the libraries listed below

• marekborowiec / spruceup
  spruceup
  ☆24Updated 8 months ago
• agmcfarland / GeneGrouper
  CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.
  ☆17Updated 6 months ago
• aaronmussig / PhyloDM
  Efficient calculation of phylogenetic distance matrices.
  ☆47Updated 7 months ago
• alvinxhan / Phydelity
  Inference of putative transmission phylogenetic clusters
  ☆11Updated 4 years ago
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆31Updated 2 years ago
• kr-colab / locator
  deep learning prediction of geographic location from individual genome sequences
  ☆50Updated 3 months ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆56Updated last year
• lskatz / Kalamari
  A curated database of completed assemblies with taxonomy IDs
  ☆44Updated 4 months ago
• evolbioinfo / pastml
  Ancestral character reconstruction and visualisation for rooted phylogenetic trees
  ☆32Updated 2 weeks ago
• LKremer / showTree
  showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.
  ☆30Updated 6 years ago
• balabanmetin / apples
  distance based phylogenetic placement
  ☆26Updated last year
• FredHutch / gig-map
  Build a map of genes present across a set of microbial genomes
  ☆14Updated 3 weeks ago
• LKremer / MSA_trimmer
  Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
  ☆17Updated 6 years ago
• simonwhelan / Divvier
  A program for divvying or partially filtering multiple sequence alignments
  ☆25Updated 5 years ago
• AlexanderLabWHOI / EUKulele
  Automatic eukaryotic taxonomic classification
  ☆28Updated last week
• bcgsc / ntEdit
  ✏️ Genome assembly polishing & SNV detection
  ☆68Updated 2 months ago
• sjspielman / phyphy
  Python HyPhy: Facilitating HyPhy execution and parsing
  ☆22Updated 3 years ago
• iqtree / iqtree3
  IQ-TREE version 3: software for phylogenetics
  ☆40Updated this week
• bcgsc / ntLink
  Minimizer-based assembly scaffolding and mapping using long reads
  ☆41Updated 7 months ago
• JLSteenwyk / ClipKIT
  a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
  ☆72Updated 2 months ago
• neherlab / treetime_examples
  A collection of documented examples using TreeTime
  ☆21Updated 5 years ago
• JLSteenwyk / orthofisher
  a broadly applicable tool for automated gene identification and retrieval
  ☆31Updated 5 months ago
• dportik / SuperCRUNCH
  A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local seq…
  ☆42Updated last year
• EBI-Metagenomics / emg-toolkit
  MGnify API toolkit
  ☆20Updated 3 months ago
• NBISweden / aMeta
  Ancient microbiome snakemake workflow
  ☆24Updated last month
• steineggerlab / unicore
  Universal and efficient core gene phylogeny with Foldseek and ProstT5
  ☆55Updated this week
• niemasd / ViralMSA
  Reference-guided multiple sequence alignment of viral genomes
  ☆68Updated 4 months ago
• ms609 / TreeDist
  Calculate distances between phylogenetic trees in R
  ☆32Updated 2 weeks ago
• rhysf / Diamond2GO
  ☆20Updated 8 months ago
• JLSteenwyk / orthohmm
  Improved Inference of Ortholog Groups using Hidden Markov Models
  ☆34Updated 2 months ago