Alternatives and similar repositories for dnds

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

• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆41Updated 2 weeks ago
• Gabaldonlab / perSVade
  perSVade: personalized Structural Variation detection
  ☆40Updated last month
• gengit / PosiGene
  ☆26Updated 4 years ago
• JLSteenwyk / orthofisher
  a broadly applicable tool for automated gene identification and retrieval
  ☆32Updated 8 months ago
• schatzlab / appliedgenomics2021
  Materials for Spring 2021 Applied Genomics Course
  ☆53Updated 4 years ago
• nanoporetech / pipeline-umi-amplicon
  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  ☆33Updated last year
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆68Updated last month
• josuebarrera / GenEra
  genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.
  ☆52Updated 9 months ago
• kjenike / panagram
  ☆64Updated last month
• JLSteenwyk / orthohmm
  Improved Inference of Ortholog Groups using Hidden Markov Models
  ☆37Updated 5 months ago
• jonassibbesen / rpvg
  Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
  ☆57Updated 7 months ago
• hsinnan75 / GSAlign
  GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
  ☆59Updated last year
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆25Updated 2 years ago
• a1ultima / hpcleap_dnds
  Sliding window dN/dS vs. functional protein domain comparison tool. Given VectorBase gene id inputs it will aggregate various useful Bioi…
  ☆18Updated 8 months ago
• rderelle / Broccoli
  orthology assignment using phylogenetic and network analyses
  ☆45Updated 5 months ago
• legumeinfo / gcv
  Federating genomes with love (and synteny derived from functional annotations)
  ☆43Updated 3 months ago
• UCSC-nanopore-cgl / MarginPolish
  MarginPolish: Graph based assembly polishing
  ☆46Updated 4 years ago
• danny-wilson / genomegaMap
  Within-species genome-wide dN/dS estimation from very many genomes
  ☆21Updated 4 years ago
• evolbioinfo / booster
  ☆27Updated 5 years ago
• dayzerodx / counterr
  ☆31Updated last year
• UCSC-LoweLab / tRNAscan-SE
  A program for detection of tRNA genes
  ☆67Updated 2 years ago
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆29Updated 2 years ago
• compgenomicslab / TreeProfiler
  tree visualization for tree + annotation data
  ☆39Updated 2 months ago
• jts / assembly_accuracy
  tools for assessing the accuracy of genome assemblies
  ☆34Updated last year
• bioforensics / pytaxonkit
  Python bindings for the TaxonKit library
  ☆41Updated 2 months ago
• cpockrandt / PhyloCSFpp
  PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…
  ☆31Updated 3 years ago
• LANL-Bioinformatics / PhaME
  Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…
  ☆33Updated last year
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• HaploKit / vechat
  Correcting errors in noisy long reads using variation graphs
  ☆52Updated 2 years ago