Aligning Coding DNA in the Presence of Frame-Shift Errors. - Lars Arvestad (CPM, 1997)

Bayesian gene/species tree reconciliation and orthology analysis using MCMC. - Lars Arvestad; Ann-Charlotte Berglund; Jens Lagergren; Bengt Sennblad (ISMB (Supplement of Bioinformatics), 2003)

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. - Lars Arvestad; Ann-Charlotte Berglund; Jens Lagergren; Bengt Sennblad (RECOMB, 2004)

Genome-Wide Survey for Biologically Functional Pseudogenes. - Örjan Svensson; Lars Arvestad; Jens Lagergren (PLoS Comput. Biol., 2006)

primetv: a viewer for reconciled trees. - Bengt Sennblad; Eva Schreil; Ann-Charlotte Berglund Sonnhammer; Jens Lagergren; Lars Arvestad (BMC Bioinform., 2007)

The gene evolution model and computing its associated probabilities. - Lars Arvestad; Jens Lagergren; Bengt Sennblad (J. ACM, 2009)

Classification of DNA sequences using Bloom filters. - Henrik Stranneheim; Max Käller; Tobias Allander; Björn Andersson; Lars Arvestad; Joakim Lundeberg (Bioinform., 2010)

Improved gap size estimation for scaffolding algorithms. - Kristoffer Sahlin; Nathaniel Street; Joakim Lundeberg; Lars Arvestad (Bioinform., 2012)

DLRS: gene tree evolution in light of a species tree. - Joel Sjöstrand; Bengt Sennblad; Lars Arvestad; Jens Lagergren (Bioinform., 2012)

Quantitative synteny scoring improves homology inference and partitioning of gene families. - Raja Ali; Sayyed Muhammad; Mehmood Alam Khan; Lars Arvestad (BMC Bioinform., 2013)

fastphylo: Fast tools for phylogenetics. - Mehmood Alam Khan; Isaac Elias; Erik Sjölund; Kristina Nylander; Roman Valls Guimera; Richard Schobesberger; Peter Schmitzberger; Jens Lagergren; Lars Arvestad (BMC Bioinform., 2013)

GenPhyloData: realistic simulation of gene family evolution. - Joel Sjöstrand; Lars Arvestad; Jens Lagergren; Bengt Sennblad (BMC Bioinform., 2013)

GAM-NGS: genomic assemblies merger for next generation sequencing. - Riccardo Vicedomini; Francesco Vezzi; Simone Scalabrin; Lars Arvestad; Alberto Policriti (BMC Bioinform., 2013)

BESST - Efficient scaffolding of large fragmented assemblies. - Kristoffer Sahlin; Francesco Vezzi; Björn Nystedt; Joakim Lundeberg; Lars Arvestad (BMC Bioinform., 2014)

Hierarchical Assembly of Pools. - Riccardo Vicedomini; Francesco Vezzi; Simone Scalabrin; Lars Arvestad; Alberto Policriti (IWBBIO (2), 2015)

Assembly scaffolding with PE-contaminated mate-pair libraries. - Kristoffer Sahlin; Rayan Chikhi; Lars Arvestad (Bioinform., 2016)

Probabilistic inference of lateral gene transfer events. - Mehmood Alam Khan; Owais Mahmudi; Ikram Ullah 004; Lars Arvestad; Jens Lagergren (BMC Bioinform., 2016)

VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces. - Raja Ali; Mikael Bark; Jorge Miró; Sayyed Muhammad; Joel Sjöstrand; Syed M. Zubair; Raja M. Abbas; Lars Arvestad (BMC Bioinform., 2017)

Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias. - Kristoffer Sahlin; Mattias Frånberg; Lars Arvestad (J. Comput. Biol., 2017)

RecPhyloXML: a format for reconciled gene trees. - Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S. Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A. Davín; Christophe Dessimoz; David Dylus; et al. (Bioinform., 2018)

alv: a console-based viewer for molecular sequence alignments. - Lars Arvestad (J. Open Source Softw., 2018)