Synteny and Rearrangement Identifier (SyRI)
...ifferences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyR...1503 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
...ds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cro...1494 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
...mplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and syn...1312 days ago
Caretta – A multiple protein structure alignment and feature extraction suite
...retta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than c...1276 days ago
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but mu...787 days ago
746 days ago
614 days ago
PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
...omes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic region...284 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
...f orthogroups. Through the use of OrthoSNAP, many additional ortholog alignments can be generated from multi-c...pecify a range of alignment filtering settings to retain high-quality alignments for phylogenetic inference. T...116 days ago
PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
...omes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic region...116 days ago