BOL

The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data...

Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multiple organisms) annotated with KEGG Orthology (KO)...

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% and large comparison studies have demonstrated both algorithms to...

genoPlotR 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, as well as home-made tabular files. Features Linear...

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 differences in genomic G+C...

I think, you can fix it by running sudo update-alternatives --remove-all python [] sudo apt install python2.7 sudo ln -sf /usr/bin/python2.7 /usr/bin/python [] python -V [] Python 2.7.12

I just came across this paper on arxiv "Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects" https://arxiv.org/abs/1308.2012 It is available at ftp://ftp.genomics.org.cn/pub/gce/

Neelam[Val] python []Python 3.5.2 (default, Nov 23 2017, 16:37:01) [GCC 5.4.0 20160609] on linuxType "help", "copyright", "credits" or "license" for more information.>>> q()Traceback (most recent call last): File "", line 1, in NameError:...

You can try many software, but the quickest one are BBTools/kmercountexact.sh To uses approximate counts: khist.sh in=reads.fq khist=khist.txt peaks=peaks.txt To uses exact counts (and thus potentially more memory) kmercountexact.sh...

Alignment algorithms http://vlab.amrita.edu/?sub=3&brch=274&sim=1431&cnt=1 #Alignments #Algo #Blast

I am working on a new genome, and wondering about prediction methods for heterozygosity in the genome. Any tools suggestions and helps are welcome. 

Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework....

Bioinformatics Laboratories https://www.crick.ac.uk/research/labs?topic=19 #Lab #Bioinfo

Bioinformatics analysis could be published in The Nucleus https://link.springer.com/journal/13237

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological...