0
Bayesian gene/species tree reconciliation and orthology analysis using MCMC
Bioinformatics (2003) 19 (suppl 1): i7-i15.
http://bioinformatics.oxfordjournals.org/content/19/suppl_1/i7.abstract
1
HGTree: database of horizontally transferred genes determined by tree reconciliation
Nucl. Acids Res. (04 January 2016) 44 (D1): D610-D619.
http://nar.oxfordjournals.org/content/44/D1/D610.full
use of Ranger-DTL
2
Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3
Mol Biol Evol (2013) 30 (8): 1987-1997.
http://mbe.oxfordjournals.org/content/30/8/1987.full
CAFE3
Download: http://www.indiana.edu/~hahnlab/software.html
Manual: http://www.indiana.edu/~hahnlab//Programs/CAFE3.0/CAFE_3.0_Manual_Aug1Update.pdf
3
BadiRate: estimating family turnover rates by likelihood-based methods
Bioinformatics (2012) 28 (2): 279-281.
http://bioinformatics.oxfordjournals.org/content/28/2/279.full
BadiRate
Download: http://www.ub.edu/softevol/badirate/
Manual: http://www2.ub.es/softevol/badirate/BadiRateManual.pdf
4
The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages
Genome Biol Evol (2014) 6 (6): 1514-1529.
http://gbe.oxfordjournals.org/content/6/6/1514.full
use of GLOOME
5
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi
PhilTransRSocB September 2015 Volume: 370 Issue: 1678
http://rstb.royalsocietypublishing.org/content/370/1678/20140335
use of Count and ALE
6
Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species
Genome Biol Evol (2015) 7 (8): 2173-2187.
http://gbe.oxfordjournals.org/content/7/8/2173.full
correction for absence of protein owing to misannotations and pseudogenization before inferring gain/loss/HGT using TFASTX (like TBLASTX)
gene gain was considered to be equivalent with HGT event
7
SylvX viewer for phylogenetic reconciliation
http://www.sylvx.org/
8
The Inference of Gene Trees with Species Trees
Syst Biol (2015) 64 (1): e42-e62.
http://sysbio.oxfordjournals.org/content/64/1/e42.full
reviewing the gene tree reconciliation problems
9
Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps
PLoS ONE 6(5): e19541.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019541
Gitools
Download: http://www.gitools.org/
Manual: http://www.gitools.org/documentation/
10
Reconciliation Approaches to Determining HGT, Duplications, and Losses in Gene Trees
Methods in Microbiology Volume 41, 2014, Pages 183?199
http://www.sciencedirect.com/science/article/pii/S0580951714000166
understanding different reconciliation methods
practical steps of using AnGST
practical steps of using Count
11
Determining the evolutionary history of gene families
Bioinformatics (2012) 28 (1): 48-55
http://bioinformatics.oxfordjournals.org/content/28/1/48.full
gain,loss
DupliPHY and DupliPHY-ML
http://www.bioinf.manchester.ac.uk/dupliphy/
Download: http://www.bioinf.manchester.ac.uk/lovell/dupliphy.html
Manual: http://www.bioinf.manchester.ac.uk/dupliphy/help.html
Step by step guide: http://www.bioinf.manchester.ac.uk/dupliphy/walkthrough.html
12
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
Bioinformatics (2010) 26 (15): 1910-1912.
http://bioinformatics.oxfordjournals.org/content/26/15/1910.full
Count
Download: http://www.iro.umontreal.ca/~csuros/gene_content/count.html
Manual: http://www.iro.umontreal.ca/~csuros/gene_content/count-usage.pdf
13
Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: The birth?death-diversification model
Theoretical Population Biology Volume 106, December 2015, Pages 22?31
http://www.sciencedirect.com/science/article/pii/S0040580915000866
understanding Birth-Death-Diversification model of gene family evolution
14
Models, algorithms and programs for phylogeny reconciliation
Brief Bioinform (2011) 12 (5): 392-400.
http://bib.oxfordjournals.org/content/12/5/392.full
