Alternatives and similar repositories for parnas

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

• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 3 months ago
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated 11 months ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆57Updated 2 months ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆40Updated last month
• tseemann / cgmlst-dists
  🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
  ☆27Updated last year
• MDU-PHL / bohra
  A pipeline for bioinformatics analysis of bacterial genomes
  ☆29Updated last month
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆28Updated 8 months ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆59Updated last week
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 6 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆51Updated 2 months ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆37Updated 3 weeks ago
• tseemann / scripts
  Miscellaneous Perl scripts from 20 years in microbial bioinformatics
  ☆17Updated 11 months ago
• iqtree / piqtree
  A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference
  ☆29Updated last week
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• JosephCrispell / homoplasyFinder
  A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
  ☆20Updated 4 years ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 years ago
• gtonkinhill / tracs
  Fast pairwise transmission inference from single genome and/or metagenomic data
  ☆21Updated 8 months ago
• virus-evolution / gofasta
  ☆36Updated 2 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated 2 years ago
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 3 months ago
• MrTomRod / scoary-2
  Calculate assocations between genes and traits
  ☆23Updated 3 months ago
• clockor2 / clockor2
  Inferring global and local strict molecular clocks using root-to-tip regression
  ☆13Updated last month
• iqbal-lab-org / pling
  Plasmid analysis using rearrangement distances
  ☆42Updated 3 weeks ago
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 8 months ago
• dhelekal / CaveDive
  ☆17Updated last year
• andrewjpage / tiptoft
  Predict plasmids from uncorrected long read data
  ☆40Updated 5 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• raufs / skDER
  skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.
  ☆45Updated last month
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆53Updated 2 years ago