LANL-Bioinformatics / PhaME
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
☆33Updated last year
Alternatives and similar repositories for PhaME:
Users that are interested in PhaME are comparing it to the libraries listed below
- ☆52Updated 3 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- Gene-flank analysis tool☆27Updated 4 months ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- STAG: Species Tree from All Genes☆34Updated 6 years ago
- reference-based long read assemblies of bacterial genomes☆48Updated 3 years ago
- SHOOT.bio - the phylogenetic search engine☆24Updated last year
- Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers☆33Updated last year
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Updated 4 years ago
- Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.☆23Updated 3 weeks ago
- Generates an NCBI .tbl file of annotations on a genome.☆66Updated 7 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- Full-length de novo viral haplotype reconstruction from noisy long reads☆18Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- ☆32Updated 4 years ago
- tools for assessing the accuracy of genome assemblies☆34Updated last year
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆41Updated 4 years ago
- metag-rev-sup☆22Updated 7 years ago
- mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads☆25Updated 2 years ago
- whole genome MLST analysis☆41Updated 3 weeks ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.☆41Updated 3 weeks ago
- ☆36Updated 3 years ago
- Genome-Genome circle synteny☆25Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆29Updated 9 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated this week