Tags: Progressive, Cactus, Whole-genome, Alignment, Package, progressiveCactus
2506 days ago
Tags: Tool, Conversion, Recover, Synteny, Blocks, Multiple, Alignment, MAF, Format, maf2synteny
2506 days ago
AVID: A Global Alignment Program
A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large synt...Tags: AVID, Global, Alignment, Program
2500 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
2317 days ago
FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a greedy way taking the symbols from the given pair ...Tags: FOGSAA, Fast, Optimal, Global, Sequence, Alignment, Algorithm
2302 days ago
Tags: CrusView, Plant, View, Visualization, See, Alignment
2177 days ago
Tags: Mapping, single, molecule, sequencing, reads, Basic, Local, Alignment, Successive, Refinement, BLASR
2136 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added utilities folder. Added support for multiple ...Tags: LSC, Improve, correct, PacBio, Long, Read, Accuracy, Short, Read, Alignment
2030 days ago
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application. lordFAST, a novel long-read mapp...Tags: lordFAST, sensitive, Fast, Alignment, Search, Tool, LOng, noisy, Read, sequencing, Data
1948 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
1865 days ago