Tags: Bioinformatics, MAF, mafTools, Alignment, Multiple
2896 days ago
Tags: Tool, Conversion, Recover, Synteny, Blocks, Multiple, Alignment, MAF, Format, maf2synteny
2534 days ago
SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit, Windows Vista 32bit, Windows 2008 Server, Window...Tags: SIMA, C++, Simultaneous, Multiple, Alignment, LC/MS, Peak, Lists
2345 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupt...Tags: MACSE, Multiple, Alignment, Coding, SEquences, Accounting, Frameshifts, Stop, Codons
1894 days ago
Mercator: Multiple Whole-Genome Orthology Map Construction
Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed ...Tags: Mercator, Multiple, Whole-Genome, Orthology, Map, Construction, orthologous, homologous, paralogous, Synteny, ancetral
1437 days ago
Mugsy: multiple whole genome alignment tool
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FA...Tags: Mugsy, multiple, whole, genome, alignment, tool
2330 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practic...Tags: Multi-CAR, tool, contig, scaffolding, multiple, references
2242 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent ...Tags: MIX, Combining, multiple, assemblies, NGS, data, Tools
2180 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference. If you are unsure which one is the appropr...Tags: GenomeMapper, Simultaneous, alignment, short, reads, multiple, genomes
2162 days ago
Tags: GRSR, tool, genome, rearrangement, scenarios, multiple, unichromosomal, genome, sequences
2036 days ago