Alternatives and similar repositories for PhyKIT

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

• davidemms / STAG
  STAG: Species Tree from All Genes
  ☆34Updated 6 years ago
• jamiemcg / BUSCO_phylogenomics
  BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
  ☆71Updated 8 months ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 4 months ago
• ThomasArn / genoPlotR_wrapper
  Wrapper for the genoPlotR R package. This wrapper makes phylogeny, genbank files and blast comparisons that is needed for the genoPLotR p…
  ☆14Updated 3 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆42Updated 7 months ago
• TheBrownLab / PhyloFisher
  PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datas…
  ☆32Updated 2 weeks ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆69Updated this week
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆48Updated 2 weeks ago
• PombertLab / SYNY
  The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
  ☆43Updated 2 months ago
• rhysf / Synima
  Synteny Imager
  ☆63Updated 10 months ago
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆58Updated 2 months ago
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆49Updated last year
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆59Updated last week
• DessimozLab / FastOMA
  FastOMA is a scalable software package to infer orthology relationship.
  ☆76Updated last week
• bcgsc / ntSynt
  Detecting multi-genome synteny using minimizer graph mapping
  ☆78Updated last month
• Gaius-Augustus / TSEBRA
  TSEBRA: Transcript Selector for BRAKER
  ☆47Updated 7 months ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆95Updated 9 months ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆42Updated 8 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• npbhavya / Kraken2-output-manipulation
  Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each col…
  ☆23Updated 11 months ago
• fethalen / Patchwork
  Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
  ☆36Updated last year
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆67Updated last month
• ccdmb / predector
  Effector prediction pipeline based on protein properties.
  ☆15Updated 9 months ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• clemgoub / dnaPipeTE
  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…
  ☆57Updated 2 years ago
• andrewgull / MGERT
  Mobile Genetic Elements Retrieving Tool
  ☆15Updated last month
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆100Updated last month
• AuReMe / emapper2gbk
  Convert GFF, fastas, annotation table and species name into Genbank.
  ☆14Updated last month
• DessimozLab / OMArk
  ☆74Updated 3 months ago