Alternatives and similar repositories for TreeCluster

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

• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆85Updated 2 years ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆86Updated 3 years ago
• neherlab / pangraph
  A bioinformatic toolkit to align genome assemblies into pangenome graphs
  ☆116Updated this week
• JLSteenwyk / ClipKIT
  a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
  ☆80Updated last month
• citiususc / veryfasttree
  Efficient phylogenetic tree inference for massive taxonomic datasets
  ☆132Updated 7 months ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 4 months ago
• deprekate / PHANOTATE
  PHANOTATE: a gene caller for phages.
  ☆78Updated 11 months ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆47Updated 2 years ago
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆59Updated 3 months ago
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆92Updated last month
• DessimozLab / FastOMA
  FastOMA is a scalable software package to infer orthology relationship.
  ☆83Updated 3 weeks ago
• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆125Updated 5 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated last month
• gatech-genemark / ProtHint
  Protein hint generation pipeline for gene finding in eukaryotic genomes
  ☆60Updated 2 years ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆62Updated 4 months ago
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆123Updated 2 months ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated 3 months ago
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆79Updated last month
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 6 months ago
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆74Updated 6 months ago
• ssolo / ALE
  Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgam…
  ☆50Updated 6 months ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆101Updated 3 years ago
• JLSteenwyk / PhyKIT
  a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
  ☆76Updated last month
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 6 months ago
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆49Updated 5 years ago
• niemasd / ViralMSA
  Reference-guided multiple sequence alignment of viral genomes
  ☆70Updated last week
• apcamargo / taxopy
  A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers
  ☆51Updated this week
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆51Updated last year
• UCSC-LoweLab / tRNAscan-SE
  A program for detection of tRNA genes
  ☆73Updated 3 years ago