Parameterizing sequence alignment with an explicit evolutionary model

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Adjusting scoring matrices to correct overextended alignments

(2013) L. J. Mills et al.   BIOINFORMATICS

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

Evolutionary inference via the Poisson Indel Process

(2012) Alexandre Bouchard-Côté et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FASTSP: linear time calculation of alignment accuracy

(2011) S. Mirarab et al.   BIOINFORMATICS

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

(2010) Y. Liu et al.   BIOINFORMATICS

Homologous over-extension: a challenge for iterative similarity searches

(2010) Mileidy W. Gonzalez et al.   NUCLEIC ACIDS RESEARCH

Quality measures for protein alignment benchmarks

(2010) Robert C. Edgar   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

SAM-T08, HMM-based protein structure prediction

(2009) K. Karplus   NUCLEIC ACIDS RESEARCH

Problems and Solutions for Estimating Indel Rates and Length Distributions

(2008) Reed A. Cartwright   MOLECULAR BIOLOGY AND EVOLUTION

Probabilistic Phylogenetic Inference with Insertions and Deletions

(2008) Elena Rivas et al.   PLoS Computational Biology

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

(2008) Sean R. Eddy   PLoS Computational Biology