PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Keywords

Biology, Stop codon, Genetics, Pseudogene, Computational biology

References

• PAML: a program package for phylogenetic analysis by maximum likelihoodZiheng Yang — 1997
• transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequencesOlaf R. P. Bininda‐Emonds — 2005
• A codon-based model of nucleotide substitution for protein-coding DNA sequences.Nick Goldman, Zefeng Yang — 1994
• Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.José Castresana — 2000
• Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its applicationTakashi Miyata, Teruo Yasunaga — 1980
• Generation and annotation of the DNA sequences of human chromosomes 2 and 4LaDeana W. Hillier, Tina Graves, Robert S. Fulton — 2005
• Dynamite: A Flexible Code Generating Language for Dynamic Programming Methods Used in Sequence ComparisonEwan Birney, Richard Durbin — 1997
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Julie Thompson, Desmond G. Higgins, Toby J. Gibson — 1994
• RevTrans: multiple alignment of coding DNA from aligned amino acid sequencesRasmus Wernersson — 2003
• The Bioperl toolkit: Perl modules for the life sciences.Jason Stajich, David E. Block, Kris Boulez — 2002
• A genome-wide survey of human pseudogenes.David Torrents — 2003

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• Identification and characterization of type III effector proteins in plant-associated bacteriaWilliam J. Thomas — 2012
• The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammalsEnrique Pardo Canalís — 2008
• Molecular biology, genetics and biochemistry of the repulsive guidance molecule familyChristopher J. Severyn, Ujwal Shinde, Peter Rotwein — 2009
• A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural TemplateMatilde Mercedes Arnay de la Rosa, José A. Torres Palenzuela — 2011
• Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced speciesJohn R. Craig — 2012
• Early Events in the Evolution of Spider Silk GenesNatividad Fernández Sola — 2012
• The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate俊一 河野, 勲 氏家 — 2012
• Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transferGraham Holter — 2014
• Bioinformatic Analysis Reveals Genome Size Reduction and the Emergence of Tyrosine Phosphorylation Site in the Movement Protein of New World Bipartite BegomovirusesEric S. Ho, Joan Kuchie, Siobain Duffy — 2014
• Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum) and Comparative Analysis with Common Buckwheat (F. esculentum)Jean M. Taylor — 2015
• Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter PopulationsW.H. Kraan — 2016
• Evolution of gremlin 2 in cetartiodactyl mammals: gene loss coincides with lack of upper jaw incisors in ruminantsStephen J. Cole — 2017
• Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.Manuel Arias Maldonado — 2017
• Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)Karunia Iriani, Meireny Meireny — 2017
• Selective pressure on the protein-coding genes of the pufferfish is correlated with phenotypic traits.Ángela Uribe Botero — 2017
• High intraspecific diversity of Restorer‐of‐fertility‐like genes in barleyV. M. Nemets, А. А. Соловьев, V. Funtov — 2018
• cRegions—a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequencesAddisu Almaw Semeneh — 2019
• Identification of Phytocyanin Gene Family in Legume Plants and their Involvement in Nodulation of Medicago truncatula.Enrique Bustamante Ramírez — 2019
• Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatumGerd Wolz, C. Gukeisen, P.S. Chopra — 2019

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