Alternatives and similar repositories for piqtree

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

• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 3 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆38Updated 2 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last week
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆69Updated this week
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆28Updated 8 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆51Updated 2 months ago
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆30Updated this week
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 11 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 4 months ago
• asmngs / asmngs20
  ASMNGS20 - 2020 Conference Details
  ☆15Updated 3 years ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆49Updated 3 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆42Updated last month
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆57Updated 2 months ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆49Updated last year
• karel-brinda / MiniPhy
  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
  ☆36Updated 2 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆40Updated last month
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆45Updated last month
• Yasas1994 / Jaeger
  Jaeger is a quick and precise tool for detecting phages in sequence assemblies.
  ☆31Updated last week
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆32Updated 5 years ago
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• mtisza1 / Cenote-Taker3
  Discover and annotate the virome
  ☆43Updated 2 months ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆59Updated last week
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated 8 months ago
• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆40Updated last week
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago