CrossMap: a program for convenient conversion of genome coordinates
...s. It’s not a program for aligning sequences to reference genome. We do not recommend using CrossMap to convert genome coordinates between species.2206 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossi...pproximate Likelihood Method", for the datasets including more than 10 species.2204 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so...2198 days ago
2225 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...-ax splice -k14 -uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minim...2186 days ago
RNA-seq Analysis Workshop Course Materials
..."types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experimen...l organisms but excludes the majority of truly biologically intereting species (e.g., Hyacinth macaw); Re...2173 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...s about its speed, accuracy and potential applications are described here: "High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries".2163 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
...ion factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA...2121 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
...then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results o...2059 days ago
swgis v2.0 : a seqword genomic island sniffer
...sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all id...2052 days ago