RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of th...1566 days ago
karyoploteR: plot whole genomes with arbitrary data
...lotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data alon...1949 days ago
2255 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
...ieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. The MMseqs2 user guide is available as Gi...2235 days ago
GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2235 days ago
ALPHA: A Toolkit for Automated Local Phylogenomic Analyses
Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It has four...2235 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
....) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set of TE families...2161 days ago
Many-to-many pairwise alignments of two sequence sets
...nus penalties arising from opening and extending gaps in the aligned sequences. The substitution matrix and gap opening and extension penalties are user-specified.2146 days ago
Digest: In silico restriction digest of complete genomes
...genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated. A tool for restriction digest of longuser's sequences is available. &n...2182 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available at:&nbs...2182 days ago