abacus-gene / pamlLinks
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs abort, etc.). Problems with input data (e.g., error/warning messages) & general questions should be posted at https://groups.google.com/g/pamlsoftware?…
☆174Updated last month
Alternatives and similar repositories for paml
Users that are interested in paml are comparing it to the libraries listed below
Sorting:
- Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation☆164Updated 3 months ago
 - Fast and accurately polish the genome generated by long reads.☆234Updated 9 months ago
 - GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆147Updated 9 months ago
 - A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0☆232Updated this week
 - Version 5 of the CAFE phylogenetics software☆148Updated 8 months ago
 - Any Way to Show Multi genomic Synteny☆209Updated 4 months ago
 - Using Deep Learning to predict gene annotations☆227Updated 2 weeks ago
 - Bacterial ribosomal RNA predictor☆259Updated 2 years ago
 - Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.☆117Updated 4 years ago
 - MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!☆271Updated 3 weeks ago
 - Tool to plot synteny and structural rearrangements between genomes☆326Updated 6 months ago
 - LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆212Updated 4 months ago
 - Processing pipeline for pan-genome visulization and exploration☆141Updated 2 years ago
 - ☆218Updated 9 months ago
 - ☆218Updated this week
 - oxford dot plots☆158Updated 3 weeks ago
 - NOVOPlasty - The organelle assembler and heteroplasmy caller☆193Updated last year
 - MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes☆132Updated 11 months ago
 - Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆158Updated 4 months ago
 - FunGAP: fungal Genome Annotation Pipeline☆111Updated 4 months ago
 - 3D de novo assembly (3D DNA) pipeline☆218Updated last year
 - MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics☆198Updated 2 months ago
 - Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆207Updated last year
 - Download files from NCBI Entrez by accession☆129Updated last year
 - ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆258Updated 3 weeks ago
 - Pan-genome wide association studies☆204Updated last year
 - A genome completeness evaluation tool based on miniprot☆227Updated last month
 - Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for…☆153Updated 6 months ago
 - Open-source usearch☆120Updated 2 months ago
 - a tool for inferring species tree from sequencing reads☆152Updated last month