Alternatives and similar repositories for SHOOT:

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

• davidemms / STAG
  STAG: Species Tree from All Genes
  ☆33Updated 6 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆36Updated 2 months ago
• chmccarthy / Pangloss
  Pangenome analysis of eukaryotes.
  ☆18Updated 4 years ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆58Updated last year
• JLSteenwyk / orthofisher
  a broadly applicable tool for automated gene identification and retrieval
  ☆30Updated 2 months ago
• brinkmanlab / islandpath
  IslandPath standalone software
  ☆31Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated last month
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆60Updated 4 years ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆42Updated last year
• PombertLab / SYNY
  The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.
  ☆40Updated 2 weeks ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆31Updated last year
• leylabmpi / SynTracker
  SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…
  ☆26Updated last week
• Gaius-Augustus / Tiberius
  Tiberius is a deep learning gene finder.
  ☆47Updated last week
• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆43Updated 6 months ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆43Updated last month
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆40Updated 3 weeks ago
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆61Updated last month
• Serka-M / Digester-MultiSequencing
  Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing
  ☆21Updated 2 years ago
• drboothtj / getphylo
  a python package for automated generation of phylogenetic trees from genbank files
  ☆20Updated last week
• UCSC-LoweLab / tRNAscan-SE
  A program for detection of tRNA genes
  ☆59Updated 2 years ago
• Sanrrone / GGisy
  Genome-Genome circle synteny
  ☆23Updated last year
• 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
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 4 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago
• balabanmetin / uDance
  ☆43Updated 10 months ago
• lauguma / GWideCodeML
  A Python package for testing evolutionary hypotheses in genome-wide approaches.
  ☆31Updated 3 years ago
• JLSteenwyk / orthohmm
  Improved Inference of Ortholog Groups using Hidden Markov Models
  ☆32Updated last month
• gengit / PosiGene
  ☆26Updated 3 years ago
• adamhockenberry / bacphlip
  A python library for predicting phage lifestyle based on genome sequence
  ☆35Updated last year