Alternatives and similar repositories for amalgkit

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

• JLSteenwyk / orthofisher
  a broadly applicable tool for automated gene identification and retrieval
  ☆32Updated last year
• bcgsc / ntSynt-viz
  Multi-genome synteny block visualization tool
  ☆52Updated 3 weeks ago
• hillerlab / ForwardGenomics
  Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework
  ☆24Updated 3 years ago
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆33Updated 3 years ago
• harta55 / EnTAP
  EnTAP is moving to GitLab for future changes https://gitlab.com/PlantGenomicsLab/EnTAP
  ☆41Updated last year
• davidemms / STAG
  STAG: Species Tree from All Genes
  ☆34Updated 7 years ago
• Rinoahu / SwiftOrtho
  A high performance tool to identify orthologs and paralogs across genomes.
  ☆27Updated 2 years ago
• KamilSJaron / k-mer-approaches-for-biodiversity-genomics
  k-mer learning materials
  ☆83Updated 11 months ago
• Adamtaranto / teloclip
  A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
  ☆50Updated 2 months ago
• rderelle / Broccoli
  orthology assignment using phylogenetic and network analyses
  ☆54Updated last week
• veg / hyphy-analyses
  HyPhy standalone analyses
  ☆52Updated 3 weeks ago
• GDKO / AvP
  Automatic evaluation of HGTs
  ☆30Updated last year
• kfuku52 / csubst
  Molecular convergence detection
  ☆46Updated 2 weeks ago
• fethalen / Patchwork
  Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
  ☆36Updated last year
• clwgg / nQuire
  A statistical framework for ploidy estimation using NGS short-read data
  ☆62Updated 7 years ago
• salzberg-lab / PSAURON
  PSAURON is a machine learning model for rapid assessment of protein coding gene annotation
  ☆52Updated last month
• formbio / FLAG
  ☆33Updated last year
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆63Updated 5 years ago
• johnssproul / RepeatProfiler
  ☆26Updated 11 months ago
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆68Updated 7 years ago
• heche-psb / wgd
  wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
  ☆37Updated 11 months ago
• MaoYafei / TREEasy
  A tool to infer species tree and phylogenetic network from multilocus data
  ☆32Updated 5 years ago
• rnajena / poseidon
  PoSeiDon: positive selection detection and recombination analysis pipeline
  ☆39Updated 4 months ago
• nf-core / genomeassembler
  Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
  ☆31Updated 2 months ago
• almeidasilvaf / syntenet
  An R package to infer and analyze synteny networks from protein sequences
  ☆36Updated 6 months ago
• bcgsc / LongStitch
  🪡Correct and scaffold assemblies using long reads
  ☆57Updated 4 months ago
• hahnlab / CAGEE
  Computational Analysis of Gene Expression Evolution
  ☆45Updated 5 months ago
• Gaius-Augustus / TSEBRA
  TSEBRA: Transcript Selector for BRAKER
  ☆49Updated 2 months ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆74Updated last week
• lh3 / hifiasm-meta
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆20Updated 5 years ago