STELLAR: fast and exact local alignments
STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar.2089 days ago
LoRMA: A tool for correcting sequencing errors in long reads
...asing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments...2081 days ago
GenomeThreader: Gene Prediction Software
...calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was...2054 days ago
Scribl : HTML5 canvas genomics graphic library
Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.2032 days ago
BamView: a free interactive display of read alignments in BAM data files
To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra command line options are given when '-h' is used: jav...2017 days ago
BLAST options, setting and defaults
...r of one-line descriptions (V) [Integer] default = 25 default = 25 default = 25 default = 25 default = 25 default = 25 Max alignments:number of alignments to show (B) [integer] defaul...1986 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...y. Identify pairs of contigs that are syntenic and move one of them to the haplotig 'pool'. The pipeline uses mapped read coverage and Minimap2 alignments to determine which contigs to...1979 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
...amework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments. HECIL’s core al...1964 days ago
GenomeView: genome browser and annotation editor
GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Loc...1963 days ago
IQ-TREE: Efficient software for phylogenomic inference
...-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring t...opping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the pro...1916 days ago