SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

IndelFR: a database of indels in protein structures and their flanking regions

(2011) Zheng Zhang et al.   NUCLEIC ACIDS RESEARCH

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

(2010) M. R. Aniba et al.   NUCLEIC ACIDS RESEARCH

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

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

AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

(2009) Surendra Kumar et al.   BMC BIOINFORMATICS

Large-Scale Parsimony Analysis of Metazoan Indels in Protein-Coding Genes

(2009) F. Belinky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins

(2008) Michael Hsing et al.   BMC BIOINFORMATICS

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

(2008) Pablo A. Goloboff et al.   CLADISTICS

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

The archaebacterial origin of eukaryotes

(2008) C. J. Cox et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE