Molecules as documents of evolutionary history, Journal of Theoretical Biology, vol.8, issue.2, pp.357-66, 1965. ,
DOI : 10.1016/0022-5193(65)90083-4
The gene tree delusion, Molecular Phylogenetics and Evolution, vol.94, pp.1-33, 2016. ,
DOI : 10.1016/j.ympev.2015.07.018
What Is the Tree of Life?, PLOS Genetics, vol.201, issue.1, p.1005912, 2016. ,
DOI : 10.1016/S0262-4079(09)60515-7
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes, Science, vol.10, issue.2, p.1258522, 2015. ,
DOI : 10.1186/1471-2148-10-9
Extensive introgression in a malaria vector species complex revealed by phylogenomics, Science, vol.316, issue.5832, p.1258524, 2015. ,
DOI : 10.1126/science.1139862
Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis, Molecular Ecology, vol.111, issue.11, pp.2361-72, 2016. ,
DOI : 10.1073/pnas.1407950111
Inversions in the Chromosomes of Drosophila Pseudoobscura, Genetics, vol.23, issue.1, pp.28-64, 1938. ,
A New Chromosomal Phylogeny Supports the Repeated Origin of Vectorial Capacity in Malaria Mosquitoes of the Anopheles gambiae Complex, PLoS Pathogens, vol.8, issue.10, p.1002960, 2012. ,
DOI : 10.1371/journal.ppat.1002960.s009
Chromosome phylogenies of malaria mosquitoes, Tsitologiia, vol.55, pp.238-278, 2013. ,
Selective introgression of paracentric inversions between two sibling species of the Anopheles gambiae complex, Genetics, vol.146, pp.239-283, 1997. ,
Adaptation through chromosomal inversions in Anopheles, Frontiers in Genetics, vol.3, issue.2, p.129, 2014. ,
DOI : 10.1371/journal.pgen.0030217
URL : http://journal.frontiersin.org/article/10.3389/fgene.2014.00129/pdf
Chromosome inversions and ecological plasticity in the main African malaria mosquitoes, Evolution, vol.19, issue.3, pp.686-701, 2017. ,
DOI : 10.1002/1097-0258(20000715)19:13<1771::AID-SIM485>3.0.CO;2-P
: the perspective from whole-genome sequencing, Molecular Ecology, vol.14, issue.23, pp.5889-906, 2016. ,
DOI : 10.18637/jss.v014.i06
Scaling up accurate phylogenetic reconstruction from gene-order data, Bioinformatics, vol.19, issue.Suppl 1, pp.305-312, 2003. ,
DOI : 10.1093/bioinformatics/btg1042
URL : https://academic.oup.com/bioinformatics/article-pdf/19/suppl_1/i305/615734/btg1042.pdf
Bayesian phylogenetic inference from animal mitochondrial genome arrangements, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.14, issue.4, pp.681-693, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a025811
Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss, Journal of Computational Biology, vol.23, issue.3, pp.150-64, 2016. ,
DOI : 10.1089/cmb.2015.0160
MLGO: phylogeny reconstruction and ancestral inference from gene-order data, BMC Bioinformatics, vol.5, issue.1, p.354, 2014. ,
DOI : 10.1371/journal.pone.0008861
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-014-0354-6?site=bmcbioinformatics.biomedcentral.com
On the PATHGROUPS approach to rapid small phylogeny, BMC Bioinformatics, vol.12, issue.Suppl 1, p.4, 2011. ,
DOI : 10.1186/1471-2105-12-S1-S4
ANGES: reconstructing ANcestral GEnomeS maps, Bioinformatics, vol.28, issue.18, pp.2388-90, 2012. ,
Reconstruction and evolutionary history of eutherian chromosomes, Proceedings of the National Academy of Sciences, vol.4, issue.27, pp.5379-5388, 2017. ,
DOI : 10.1007/s004390100535
Sequence assembly demystified, Nature Reviews Genetics, vol.23, issue.3, pp.157-67, 2013. ,
DOI : 10.1093/bioinformatics/btm451
Repetitive DNA and next-generation sequencing: computational challenges and solutions, Nature Reviews Genetics, vol.18, issue.1, pp.36-46, 2011. ,
DOI : 10.1093/dnares/dsq028
URL : http://europepmc.org/articles/pmc3324860?pdf=render
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing, Nature Biotechnology, vol.45, issue.6, pp.623-653, 2015. ,
DOI : 10.1186/gb-2004-5-2-r12
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017. Epub ahead of print ,
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage, Genome Research, vol.26, issue.3, pp.342-50, 2016. ,
DOI : 10.1101/gr.193474.115
Every genome sequence needs a good map, Genome Research, vol.19, issue.11, pp.1925-1933, 2009. ,
DOI : 10.1101/gr.094557.109
URL : http://genome.cshlp.org/content/19/11/1925.full.pdf
ALLMAPS: robust scaffold ordering based on multiple maps, Genome Biology, vol.16, issue.1, p.3, 2015. ,
DOI : 10.1093/bioinformatics/bth168
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-014-0573-1?site=genomebiology.biomedcentral.com
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools, Frontiers in Genetics, vol.6, p.220, 2015. ,
DOI : 10.3389/fgene.2015.00220
URL : https://www.frontiersin.org/articles/10.3389/fgene.2015.00220/pdf
ABACAS: algorithm-based automatic contiguation of assembled sequences, Bioinformatics, vol.33, issue.suppl_2, pp.1968-1977, 2009. ,
DOI : 10.1093/nar/gki356
Reordering contigs of draft genomes using the Mauve Aligner, Bioinformatics, vol.33, issue.16, pp.2071-2074, 2009. ,
DOI : 10.1093/nar/gki356
SIS: a program to generate draft genome sequence scaffolds for prokaryotes, BMC Bioinformatics, vol.13, issue.1, p.96, 2012. ,
DOI : 10.1128/JB.01202-08
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references, Bioinformatics, vol.29, issue.21, pp.319-347, 2014. ,
DOI : 10.1093/bioinformatics/btt476
URL : https://academic.oup.com/bioinformatics/article-pdf/30/12/i319/1103957/btu291.pdf
CAR: contig assembly of prokaryotic draft genomes using rearrangements, BMC Bioinformatics, vol.65, issue.5, p.381, 2014. ,
DOI : 10.1016/S0022-0000(02)00011-9
Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences, GigaScience, vol.43, issue.D1, p.38, 2016. ,
DOI : 10.1093/nar/gku1177
URL : https://academic.oup.com/gigascience/article-pdf/5/1/1/10843864/13742_2016_Article_141.pdf
Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology, PLOS ONE, vol.13, issue.6, pp.1-19, 2016. ,
DOI : 10.1371/journal.pone.0155459.s006
Phylogenetic comparative assembly, Algorithms for Molecular Biology, vol.5, issue.1, p.3, 2010. ,
DOI : 10.1186/1748-7188-5-3
URL : http://europepmc.org/articles/pmc2826331?pdf=render
Reference-assisted chromosome assembly, Proceedings of the National Academy of Sciences, vol.12, issue.6, pp.1785-90, 2013. ,
DOI : 10.1101/gr.229102. Article published online before print in May 2002
URL : http://www.pnas.org/content/110/5/1785.full.pdf
Ragout--a reference-assisted assembly tool for bacterial genomes, Bioinformatics, vol.19, issue.6, pp.302-311, 2014. ,
DOI : 10.1101/gr.089532.108
URL : https://academic.oup.com/bioinformatics/article-pdf/30/12/i302/1097844/btu280.pdf
Multigenome scaffold co-assembly based on the analysis of gene orders and genomic repeats, pp.237-249, 2016. ,
MeDuSa: a multi-draft based scaffolder, Bioinformatics, vol.31, issue.15, pp.2443-51, 2015. ,
DOI : 10.1093/nar/gki356
URL : https://hal.archives-ouvertes.fr/hal-01139506
Mosaic Genome Architecture of the Anopheles gambiae Species Complex, PLoS ONE, vol.35, issue.2, p.1249, 2007. ,
DOI : 10.1371/journal.pone.0001249.s010
A Polytene Chromosome Analysis of the Anopheles gambiae Species Complex, Science, vol.298, issue.5597, pp.1415-1423, 2002. ,
DOI : 10.1126/science.1077769
Multiple origins of cytologically identical chromosome inversions in the Anopheles gambiae complex, Genetics, vol.150, pp.807-821, 1998. ,
Attempts to molecularly distinguish cryptic taxa in Anopheles gambiae s.s., Insect Molecular Biology, vol.68, issue.1, pp.25-32, 2001. ,
DOI : 10.1016/0035-9203(74)90035-2
Are chromosomal inversions induced by transposable elements? A paradigm from the malaria mosquito Anopheles gambiae, Parassitologia, vol.41, pp.119-142, 1999. ,
Species composition and inversion polymorphism of the Anopheles gambiae complex in some sites of Ghana, West Africa, Acta Tropica, vol.56, issue.1, pp.15-23, 1994. ,
DOI : 10.1016/0001-706X(94)90036-1
Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, issue.12, pp.1557-65, 2006. ,
DOI : 10.1101/gr.5383506
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes, PLoS Computational Biology, vol.48, issue.11, p.1000234, 2008. ,
DOI : 10.1371/journal.pcbi.1000234.t003
URL : https://hal.archives-ouvertes.fr/inria-00269397
Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol.12, issue.Suppl. 1, pp.382-388, 2012. ,
DOI : 10.1186/1471-2105-12-S1-S4
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach, BMC Bioinformatics, vol.16, issue.Suppl 19, p.6, 2015. ,
DOI : 10.1186/1471-2105-16-S19-S6
URL : https://hal.archives-ouvertes.fr/hal-01245495
Ancestral gene synteny reconstruction improves extant species scaffolding, BMC Genomics, vol.16, issue.Suppl 10, p.11, 2015. ,
DOI : 10.1186/1471-2164-16-S10-S11
URL : https://hal.archives-ouvertes.fr/hal-01180303
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies, Genome Biology and Evolution, vol.62, issue.1, pp.1312-1319, 2017. ,
DOI : 10.1093/sysbio/sys076
URL : https://hal.archives-ouvertes.fr/hal-01503766
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1., Bioinformatics, vol.2014, issue.13, pp.2056-2058, 2016. ,
DOI : 10.1109/TCBB.2010.14
URL : https://academic.oup.com/bioinformatics/article-pdf/32/13/2056/16920517/btw105.pdf
Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, vol.13, p.11, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00773071
ScaffMatch: scaffolding algorithm based on maximum weight matching, Bioinformatics, vol.31, issue.16, pp.2632-2640, 2015. ,
DOI : 10.1101/gr.074492.107
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software, Nucleic Acids Research, vol.3, issue.Suppl. 2, pp.250-256, 2015. ,
DOI : 10.1093/gbe/evq083
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.21, issue.21, pp.2688-90, 2006. ,
DOI : 10.1093/bioinformatics/bti191
Efficient Gene Tree Correction Guided by Genome Evolution, PLOS ONE, vol.17, issue.12, p.159559, 2016. ,
DOI : 10.1371/journal.pone.0159559.s001
URL : https://hal.archives-ouvertes.fr/hal-01162963
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.18, issue.15, p.2114 ,
DOI : 10.1101/gr.074492.107
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366 ,
DOI : 10.1093/bioinformatics/btp352
URL : http://europepmc.org/articles/pmc3322381?pdf=render
BESST - Efficient scaffolding of large fragmented assemblies, BMC Bioinformatics, vol.15, issue.1, p.281, 2014. ,
DOI : 10.1186/1471-2105-15-281
Genome scaffolding with PE-contaminated mate-pair libraries. bioRxiv preprint, pp.1-13, 2015. ,
DOI : 10.1101/025650
URL : https://hal.archives-ouvertes.fr/hal-01236176
Informed and automated k-mer size selection for genome assembly, Bioinformatics, vol.18, issue.5, pp.31-38, 2014. ,
DOI : 10.1101/gr.074492.107
URL : https://hal.archives-ouvertes.fr/hal-01477511
Space-efficient and exact de Bruijn graph representation based on a Bloom filter, Algorithms for Molecular Biology, vol.8, issue.1, p.22, 2013. ,
DOI : 10.1101/gr.131383.111
URL : https://hal.archives-ouvertes.fr/hal-00753930
Chromosome evolution in malaria mosquitoes inferred from physically mapped genome assemblies, Journal of Bioinformatics and Computational Biology, vol.161, issue.3, p.1630003, 2016. ,
DOI : 10.1534/genetics.110.123059
Conundrum of jumbled mosquito genomes, Science, vol.482, issue.7384, pp.27-35, 2015. ,
DOI : 10.1038/nature10811
Chromosomal plasticity and evolutionary potential in the malaria vector Anopheles gambiae sensu stricto: insights from three decades of rare paracentric inversions, BMC Evolutionary Biology, vol.8, issue.1, p.309, 2008. ,
DOI : 10.1186/1471-2148-8-309
Breaking good: accounting for the diversity of fragile regions for estimating rearrangement distances ,
What is the difference between the breakpoint graph and the de Bruijn graph?, BMC Genomics, vol.15, issue.Suppl 6, p.6, 2014. ,
DOI : 10.1101/gr.757503
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies, PLoS Computational Biology, vol.25, issue.12, p.1003998, 2014. ,
DOI : 10.1371/journal.pcbi.1003998.s001
Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences, Systematic Zoology, vol.28, issue.2, pp.132-63, 1979. ,
DOI : 10.2307/2412519