Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
...o;fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species that were the common ancestors of extant species from across the tree of life....2055 days ago
SISRS: Site Identification from Short Read Sequences
Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.2029 days ago
Genome sequence-based (sub-)species delineation.
The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates diff...2015 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96%...2015 days ago
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UPhO: Scripts for homology and orthology assessment from genomic sequences.
...ncies. Type UPhO.py -h for help. The only input requierement for UPhO is a tree (or trees) in Newick format in which the leaves are named with a species idenfifier, a field separator...1982 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specif...1965 days ago
iRNAD: a computational tool for identifying D modification sites in RNA sequence
iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. http://lin-group.cn/server/iRNAD/1860 days ago
Retrieving Taxonomic Information with R
...d in myTAI can be used to classify genomes according to phylogenetic classification into Phylostrata (Phylostratigraphy) or to retrieve species specific taxonomic informatio...1755 days ago