AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

PROCAIN: protein profile comparison with assisting information

(2009) Yong Wang et al.   NUCLEIC ACIDS RESEARCH

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The effectiveness of position- and composition-specific gap costs for protein similarity searches

(2008) A. Stojmirovic et al.   BIOINFORMATICS

Profile Comparer: a program for scoring and aligning profile hidden Markov models

(2008) M. Madera   BIOINFORMATICS

Multiple protein sequence alignment

(2008) Jimin Pei   CURRENT OPINION IN STRUCTURAL BIOLOGY

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

Accurate statistical model of comparison between multiple sequence alignments

(2008) Ruslan I. Sadreyev et al.   NUCLEIC ACIDS RESEARCH

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology