presentation describing ale, a suite of programs for gene tree reconstruction in the presence of...
DESCRIPTION
ALE is a series of programs for inferring high quality gene trees in the presence of gene duplication, transfer, and loss. It is based on Amalgamated Likelihood Estimation and a probabilistic model of gene duplication, transfer and loss.TRANSCRIPT
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Using ALE to reconstruct gene treesALE is developed by Gergely Szöllősi [email protected] @sllsi
Mistakes due to Bastien Boussau @Bastounette
Presentation available on slideshare: http://www.slideshare.net/
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References• Phylogenetic modeling of lateral gene transfer reconstructs the
pattern and relative timing of speciations. Szöllősi GJ, Boussau B, Abby SS, Tannier E, Daubin V. Proc Natl Acad Sci U S A. 2012 109(43):17513-8. doi: 10.1073/pnas.1202997109.
• Lateral gene transfer from the dead. Szöllősi GJ, Tannier E, Lartillot N, Daubin V. Syst Biol. 2013 62(3):386-97. doi: 10.1093/sysbio/syt003.
• Efficient exploration of the space of reconciled gene trees. Szöllősi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V. Syst Biol. 2013 62(6):901-12. doi: 10.1093/sysbio/syt054.
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Model and ALE program• Birth-death probabilistic model including:
• gene duplication (D)
• gene loss (L)
• gene transfer (T)
• Given (one or more) gene trees and an ultrametric species tree, returns:
• a reconciled gene tree, annotated with D,T,L events
• its Likelihood
• optimized rates of D,T,L events
• Can return ML estimate, or sample according to likelihood
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T IM E
Transfers tread beyond the represented species phylogeny
Lateral gene transfer from the dead. Szöllosi GJ, Tannier E, Lartillot N, Daubin V. Syst Biol. 2013 62(3):386-97. doi: 10.1093/sysbio/syt003.
![Page 5: Presentation describing ALE, a suite of programs for gene tree reconstruction in the presence of gene duplication, transfer and loss](https://reader033.vdocuments.us/reader033/viewer/2022042607/55849e49d8b42ac1328b52c7/html5/thumbnails/5.jpg)
T IM E
Transfers tread beyond the represented species phylogeny
Lateral gene transfer from the dead. Szöllosi GJ, Tannier E, Lartillot N, Daubin V. Syst Biol. 2013 62(3):386-97. doi: 10.1093/sysbio/syt003.
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T IM E
Mathematically, most transfers involve unrepresented lineages
Transfers tread beyond the represented species phylogeny
Lateral gene transfer from the dead. Szöllosi GJ, Tannier E, Lartillot N, Daubin V. Syst Biol. 2013 62(3):386-97. doi: 10.1093/sysbio/syt003.
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ALE download and installation
• 2 ways:
1. use a virtual image through VirtualBox:"
• download ftp://www.prabi.fr/pub/ancestrome/ALE-demo.ova
• while downloading, if necessary, install both VirtualBox and VirtualBox additions (on virtualbox website (https://www.virtualbox.org/); be careful to choose the right version for your system);
• run VirtualBox, and do File / Import a Virtual Application. Then, select the downloaded file;
2. Install it in full:"
• download it from https://github.com/ssolo/ALE
• Follow the instructions in the README.md file
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ALE pipeline• Examples can be found in the example_data folder
• Generate gene tree distribution (e.g. PhyloBayes, mrBayes, revBayes…), then
• use ALEobserve on the tree distribution:
!./ALEobserve_LINUX HBG745965_real.1.treelist 1000!
• use ALEml if you want to get the ML estimate of the reconciled gene tree
! ./ALEml S.tree HBG745965_real.1.treelist.ale!
• use ALEsample if you want to get a sample of reconciled gene trees
! ./ALEsample S.tree HBG284202_real.ale!
• Look at the annotations written as bootstrap values (e.g. NJplot)
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Species tree
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Reconciled PhyML gene
tree
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Reconciled PhyML gene
tree
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Reconciled PhyML gene
tree
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Reconciled PhyML gene
tree
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Reconciled PhyML gene
tree
Many (8) transfers in the PhyML tree
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Reconciled Amalgamated
gene tree
ACAM1_1_PE135CYAP4_1_PE420THEEB_1_PE1494
GLVIO1_1_PE1169SYNJB_1_PE950SYNJA_1_PE2030.3
.26
@25|20.20
T@26|26
TRIEI_1_PE668NOSP7_2_PE4607ANAVT_4_PE931ANASP_6_PE2969.6.18
SYNY3_4_PE2642SYNP6_1_PE1291SYNE7_1_PE221
SYNR3_2_PE944PROMM_1_PE495PROM3_1_PE1845
PROM4_1_PE1056PRMAR1_1_PE1063PROMT_1_PE635PROM1_1_PE651
PROM9_1_PE623PROM2_1_PE676PROMS_1_PE651PROM0_1_PE623.7
.8
PROM5_1_PE662PROMP_1_PE651
.9
.5
.2
.10
.14
.16
.4
.17
SYNPW_2_PE774SYNS3_1_PE1833SYNPX_1_PE1481SYNSC_1_PE1008SYNS9_1_PE925
.12
.11
.13
.21
.19
.22
@22|1.1
.23
Tb@23|23
MICAN_1_PE2716CYAP7_1_PE2280CYAA5_6_PE594CYAP8_1_PE2632
.24
.15
T@23|SYNY3
.25
.31
.30.29
.33:0
.27
.32
0.2
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Reconciled Amalgamated
gene tree
ACAM1_1_PE135CYAP4_1_PE420THEEB_1_PE1494
GLVIO1_1_PE1169SYNJB_1_PE950SYNJA_1_PE2030.3
.26
@25|20.20
T@26|26
TRIEI_1_PE668NOSP7_2_PE4607ANAVT_4_PE931ANASP_6_PE2969.6.18
SYNY3_4_PE2642SYNP6_1_PE1291SYNE7_1_PE221
SYNR3_2_PE944PROMM_1_PE495PROM3_1_PE1845
PROM4_1_PE1056PRMAR1_1_PE1063PROMT_1_PE635PROM1_1_PE651
PROM9_1_PE623PROM2_1_PE676PROMS_1_PE651PROM0_1_PE623.7
.8
PROM5_1_PE662PROMP_1_PE651
.9
.5
.2
.10
.14
.16
.4
.17
SYNPW_2_PE774SYNS3_1_PE1833SYNPX_1_PE1481SYNSC_1_PE1008SYNS9_1_PE925
.12
.11
.13
.21
.19
.22
@22|1.1
.23
Tb@23|23
MICAN_1_PE2716CYAP7_1_PE2280CYAA5_6_PE594CYAP8_1_PE2632
.24
.15
T@23|SYNY3
.25
.31
.30.29
.33:0
.27
.32
0.2
Amalgamation of gene trees leads to fewer transfers (3)
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In progress…
• STRALE: • A Bayesian probabilistic method that can interpret thousands of
gene trees with DTL events and reconstruct a time-ordered species tree
• Currently undergoing tests • Can run on thousands of gene families (parallel architecture) • Will be open access • Can run on dozens of species