Showing 3 of total 3 results (show query)
ropensci
phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
Maintained by Shixiang Wang. Last updated 9 months ago.
blastngenbankpeer-reviewedphylogeneticssequence-alignment
23 stars 5.86 score 156 scripts
nanxstats
ssw:Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD
Provides an R interface for 'SSW' (Striped Smith-Waterman) via its 'Python' binding 'ssw-py'. 'SSW' is a fast 'C' and 'C++' implementation of the Smith-Waterman algorithm for pairwise sequence alignment using Single-Instruction-Multiple-Data (SIMD) instructions. 'SSW' enhances the standard algorithm by efficiently returning alignment information and suboptimal alignment scores. The core 'SSW' library offers performance improvements for various bioinformatics tasks, including protein database searches, short-read alignments, primary and split-read mapping, structural variant detection, and read-overlap graph generation. These features make 'SSW' particularly useful for genomic applications. Zhao et al. (2013) <doi:10.1371/journal.pone.0082138> developed the original 'C' and 'C++' implementation.
Maintained by Nan Xiao. Last updated 6 months ago.
bioinformaticsreticulatesequence-alignmentsimdsmith-waterman
6 stars 5.18 score
mhahsler
rMSA:Interface for Popular Multiple Sequence Alignment Tools
Seamlessly interfaces the Multiple Sequence Alignment software packages ClustalW, MAFFT, MUSCLE and Kalign (downloaded separately) and provides support to calcualte distances between sequences. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
Maintained by Michael Hahsler. Last updated 10 months ago.
geneticssequencinginfrastructurealignmentbioinformaticssequence-alignment
12 stars 3.78 score 7 scripts