Alternatives and similar repositories for santa-sim

Users that are interested in santa-sim are comparing it to the libraries listed below

• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆89Updated last year
• NicolaDM / MAPLE
  MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.
  ☆51Updated this week
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆78Updated 2 months ago
• benjaminhgood / LTEE-metagenomic
  Time-resolved metagenomic sequencing of Lenski's long-term evolution experiment with Escherichia coli
  ☆22Updated 6 years ago
• thednainus / Bayesian_tutorial
  Tutorial on Bayesian phylogenetic analysis
  ☆47Updated 8 years ago
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated 3 weeks ago
• lonelyjoeparker / befi-bats-gui
  Java software to analyse phylogeny-trait correlations in discrete traits, accounting for phylogenetic uncertainty via posterior sampling.
  ☆12Updated 8 years ago
• OrthoFinder / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆58Updated this week
• evolbioinfo / booster
  ☆27Updated 5 years ago
• W-L / ProblematicSites_SARS-CoV2
  ☆49Updated 3 years ago
• niemasd / ViralMSA
  Reference-guided multiple sequence alignment of viral genomes
  ☆70Updated 4 months ago
• evolbioinfo / pastml
  Ancestral character reconstruction and visualisation for rooted phylogenetic trees
  ☆36Updated 4 months ago
• lskatz / awesome-bioinformatics-education
  resources for bioinformatics education
  ☆87Updated 4 months ago
• drostlab / orthologr
  Genome wide orthology inference and dNdS estimation
  ☆96Updated last month
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆57Updated 4 years ago
• mourisl / Rcorrector
  Error correction for Illumina RNA-seq reads
  ☆67Updated last year
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆85Updated last year
• SamStudio8 / reticulatus
  A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
  ☆68Updated 3 years ago
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 3 months ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆49Updated 3 years ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆63Updated 2 years ago
• fmenardo / Treemmer
  Python tool to reduce size and redundancy of phylogenetic datasets
  ☆45Updated 2 years ago
• steineggerlab / conterminator
  Detection of incorrectly labeled sequences across kingdoms
  ☆85Updated 2 years ago
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 5 months ago
• jonas-fuchs / BAMdash
  create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
  ☆54Updated last month
• rega-cev / virulign
  VIRULIGN: fast codon-correct alignment and annotation of viral genomes
  ☆35Updated 4 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆32Updated last month
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆104Updated 8 months ago
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆25Updated 2 years ago