BLAST options, setting and defaults
...t al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is be...1966 days ago
genoPlotR - plot gene and genome maps project!
...is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results...1964 days ago
1934 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_...1932 days ago
SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplica...1925 days ago
BUSCA: an integrative web server to predict subcellular localization of proteins
...ent Annotator) is a web-server for predicting protein subcellular localization. BUS...fferent tools to predict localization-related protein features (DeepSig, TPpred3, P...ar localization of both globular and membrane proteins (BaCelLo, MemLoci and SChlor...1906 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
...translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containi...1896 days ago
IQ-TREE: Efficient software for phylogenomic inference
...he tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. How...1896 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
...set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putative functions to gene calls using protein-, virus-, and phage-centric d...1809 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Marko...1754 days ago