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Mulan: MUltiple sequence Local AligNment and conservation visualization tool
By Rahul Nayak 2694 days agomulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 2560 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...
Ancestral sequence reconstruction steps !
Last updated 2392 days ago by Surabhi Chaudhary Comments (1)Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2238 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...iRNAD: a computational tool for identifying D modification sites in RNA sequence
By Abhimanyu Singh 2030 days agolin-group.cn - 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...Apollo: a sequence annotation editor
By Abhimanyu Singh 1926 days agogenomebiology.biomedcentral.com - The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting...GfaViz: flexible and interactive visualization of GFA sequence graphs
By Jit 1777 days agogithub.com - GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general,...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1751 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 1609 days agogithub.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...Kmer: a suite of tools for DNA sequence analysis
By BioStar 1205 days agohelp.rc.ufl.edu - More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparision tool: Comparative mapping between two genome assemblies (same species), or between two different genomes (cross...
