SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization

(2015) Andres Veidenberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Indel Reliability in Indel-Based Phylogenetic Inference

(2014) Haim Ashkenazy et al.   Genome Biology and Evolution

Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies

(2014) Eli Levy Karin et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

(2014) E. J. P. Douzery et al.   MOLECULAR BIOLOGY AND EVOLUTION

A synchronized global sweep of the internal genes of modern avian influenza virus

(2014) Michael Worobey et al.   NATURE

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

(2012) Ari Löytynoja et al.   BIOINFORMATICS

REvolver: Modeling Sequence Evolution under Domain Constraints

(2012) Tina Koestler et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model

(2012) Patrick Kück et al.   PLoS One

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Measuring the distance between multiple sequence alignments

(2011) B. P. Blackburne et al.   BIOINFORMATICS

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees

(2011) Fernando Izquierdo-Carrasco et al.   BMC BIOINFORMATICS

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

(2011) Botond Sipos et al.   BMC BIOINFORMATICS

Selection-Driven Divergence After Gene Duplication in Arabidopsis thaliana

(2011) Toni I. Gossmann et al.   JOURNAL OF MOLECULAR EVOLUTION

ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods

(2011) Minh Anh Thi Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution

(2010) Itay Mayrose et al.   MOLECULAR BIOLOGY AND EVOLUTION

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

(2008) Liat Shavit Grievink et al.   BMC EVOLUTIONARY BIOLOGY

Simulating DNA Coding Sequence Evolution with EvolveAGene 3

(2008) B. G. Hall   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2008) A. Loytynoja et al.   SCIENCE