lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
...rror rates. lordFAST is specially designed for aligning reads from PacBio sequenci...gy but provides the user the ability to change alignment parameters depending on t...g-read mapper that is specifically designed to align reads generated by PacBio and...1985 days ago
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BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul...atch is the best choice. Another sequence alignment tool that may yield diffe...ault = 25 default = 25 default = 25 Max alignments:number of alignments to...1972 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA tran...ns. MACSE is hence the first automatic solution to align protein-coding gene datasets...ed frameshifts in public database sequences and in aligning next-generation sequencing...1902 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
...els using an EM algorithm Mining candidate STR alleles from population-scale sequencing data Employing a specialized hidden Markov model to align reads to candidate alleles wh...1884 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment,...1866 days ago
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ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A...1655 days ago
Kalign: fast multiple sequence alignment program for biological sequences.
Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align s...align -i BB11001.tfa -f clu -o out.clu Re-align sequences in an existing alig...1646 days ago