List of visualization tools for network biology
Network analysis is any structured technique used to mathematic...e listed here https://bmcbioinformatics.biomedcentral.com/articles/s...inetics stochastic simulation software http://magnet.systemsbiology.net/software/Dizzy/ DyCoNet Gephi p...http://arcadiapathways.sourceforge.net/...2286 days ago
List of visualization tools for genome alignments
Genome browsers are useful not only for showing final results but also for improving analysis protocols,...data http://www.bcgsc.ca/platform/bioinfo/software/abyss-explorer BamView...riation http://lookseq.sourceforge.net MagicViewer Vis...ization software http://bioinfor.com/zoo...2282 days ago
Computational resources for TE discovery and TE detection
Transposable Elements (TEs) to genome structure and evolution as wel...est in developing new methods for their computational analysis. Fo...tp://jaketu.biochem.vt.edu/dl_software.htm HMMER http://hmmer...tp://www.eecs.wsu.edu/~ananth/software.htm MAK http://wessler...eat-match http://mummer.sourceforge....2272 days ago
Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes
Horizontal gene transfer (HGT), the “non-sexual movement of genetic materia...far rarer in multicellular eukaryotes. In order for a eukaryotic species to gain a gene by HGT, foreig...f the donor and the host. Over the longer term, foreign DNA...848 days ago
Some useful Bioinformatics links
Reference-free prediction of rearrangement breakpoint reads | Bioinformatics | Oxford Academic https://academic.oup.co...tps://mafft.cbrc.jp/alignment/software/tips.html Omega | Overla...o/Bandage/ Codon Optimization OnLine (COOL): a web-based multi-...tml Dot: Interactive dot plot for genome-...2240 days ago
Ligand Docking Tools and Software !
Ligand docking referred to cases where small molecule (“ligand&r...following is partial list of docking software, focusing on free (at least for academic institutes) and/or p...matic (IC) Flexible ligandDOCK 3.5 (force...veral studies have shown that the performance of...2200 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo asse.... Take a look at the PRICE software from the DeRisi lab. Its...asetools-a-wide-range-of-bioinformatics-solutions/sspacev12/),...://www.sanger.ac.uk/resources/software/pagit/ In particular...2163 days ago
Ancestral sequence reconstruction steps !
Ancestral sequence reconstruction (ASR) – also known as...d Zuckerkandl. Some early efforts were made in the eighties-n...p;http://mafft.cbrc.jp/alignment/software/source.html" mafft --ma...enetic signal, is possible to perform w...based groups. 4.3- RDP4 for downloa...2177 days ago
List of non-commercial NGS genotype-calling software
Meaningful analysis of next-generation sequencing (NGS) data, which...ta. A list of programs for genotype and SNP calling : SOAP2&...-sample Aligned reads Package for aligned NGS data analysis, wh...te SNPs, genotype likelihoods Software for imputation, phasing...2094 days ago
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