SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitiv...to interpret similarity pairs as edges of a network. A very efficient algorithm...2023 days ago
EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficie...comparisons and analyses. Two of the core features are: a function prediction algorithm...2021 days ago
2018 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines...cision weights obtained from short read alignments. HECIL’s core algorithm...2003 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a th...e-step normalization procedure with a novel heterogeneous hidden Markov model algorithm...2000 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome...cts all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm...1991 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...gainst a reference coding sequence. For further details about the underlying algorithm...1955 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoo...1955 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes....ishes this by: Learning locus-specific PCR stutter models using an EM algorithm...1938 days ago
1901 days ago