Alternatives and similar repositories for pasta

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

• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆61Updated 6 years ago
• JLSteenwyk / ClipKIT
  a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
  ☆80Updated last month
• microgenomics / tutorials
  In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…
  ☆84Updated 7 years ago
• KatyBrown / CIAlign
  ☆132Updated last year
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆124Updated 3 months ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆75Updated last year
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆49Updated 5 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆116Updated last year
• kjolley / BIGSdb
  Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
  ☆73Updated this week
• fhcrc / seqmagick
  An imagemagick-like frontend to Biopython SeqIO
  ☆116Updated last year
• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆89Updated 3 weeks ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆47Updated 2 years ago
• ddarriba / modeltest
  Best-fit model selection
  ☆85Updated last year
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆79Updated 2 years ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆86Updated 3 years ago
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆112Updated last year
• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆125Updated 6 months ago
• glarue / jgi-query
  A simple command-line tool to download data from Joint Genome Institute databases
  ☆52Updated 2 years ago
• epruesse / SINA
  SINA - Reference based multiple sequence alignment
  ☆41Updated 4 years ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆50Updated 3 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated 3 months ago
• citiususc / veryfasttree
  Efficient phylogenetic tree inference for massive taxonomic datasets
  ☆132Updated 7 months ago
• SPAAM-community / AncientMetagenomeDir
  Repository containing lists of all published ancient metagenomic (and related) samples and libraries
  ☆77Updated this week
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆121Updated 3 weeks ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆85Updated 2 years ago
• qiyunzhu / woltka
  Woltka: a versatile meta'omic data classifier
  ☆75Updated 2 months ago