Alternatives and similar repositories for piqtree

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

• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆46Updated 10 months ago
• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆49Updated this week
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆84Updated 2 weeks ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆47Updated 3 months ago
• rrwick / Verticall
  Recombination-free trees
  ☆63Updated 5 months ago
• bede / hostile
  Precise host read removal
  ☆115Updated 5 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆67Updated 3 years ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆52Updated this week
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated 3 months ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆48Updated 2 months ago
• bluenote-1577 / myloasm
  A new high-resolution long-read metagenome assembler for even noisy reads
  ☆121Updated this week
• mbhall88 / NanoVarBench
  Evaluating Nanopore-based bacterial variant calling
  ☆21Updated 6 months ago
• compgenomicslab / TreeProfiler
  tree visualization for tree + annotation data
  ☆49Updated 7 months ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆78Updated 5 months ago
• susiegriggo / Phynteny
  Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny
  ☆58Updated 8 months ago
• refresh-bio / vclust
  Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes
  ☆97Updated 8 months ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆104Updated last week
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆80Updated 2 years ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆40Updated 4 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆63Updated 9 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• Yasas1994 / Jaeger
  Jaeger is a quick and precise tool for detecting phages in sequence assemblies.
  ☆35Updated 2 weeks ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆46Updated 3 weeks ago
• rhysnewell / Lorikeet
  Strain resolver for metagenomics
  ☆80Updated last year
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆98Updated 2 weeks ago
• AllTheBacteria / AllTheBacteria
  Follow up to Grace Blackwell's 661k dataset, for 2023
  ☆130Updated this week
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆48Updated last week
• zreitz / multismash
  A workflow and scripts for large-scale antiSMASH analyses
  ☆46Updated 10 months ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆33Updated 6 years ago