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Evolution
Containing computational routines to support article titled "Undersampling and the inference of coevolution in proteins"
genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.
Cython bindings and Python interface to HMMER3.
FAS - Tool for Feature Architecture Similarity calculation
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact o…
Detection of the structural, evolutionary and functional relationship between different proteins and protein families requires comparative analysis of their amino acid sequences through multiple se…
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Official home of genome aligner based upon notion of Cactus graphs
DNA multiple sequence aligner, official version from Penn State's Miller Lab
Flexible protein structural alignment based on Protein Units
Source code for iDeLUCS. An interactive deep-learning based tool for clustering of genomic sequences
GERONIMO: GEnomic RNA hOmology aNd evolutIonary MOdeling
Cross Species Investigation and Analysis : an R package that provides an alternative framework for cross-species transcriptomic comparison of non-diseased wild-type RNA sequencing gene expression d…
lncHOME (lncRNA Homology Explorer), a computational pipeline that identifies a unique coPARSE-lncRNA class with conserved genomic locations and patterns of RNA binding protein (RBP) binding sites.
LAMBDA – the Local Aligner for Massive Biological DatA
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
⚙️TPMA: a two pointers meta-alignment tool to ensemble different nucleic acid multiple sequence alignment results
Some code to experiment around the different notions of distances to solve the small parsimony problem on RNA structures.
Approximate nearest neighbour search for microbial genomes based on hash metric
HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors
gapped-kmer based whole genome alignment software