[R-sig-phylo] Boostrap and likelihood values on branches

Gwennaël Bataille gwennael.bataille at uclouvain.be
Mon Mar 12 10:34:51 CET 2012


Dear all,
I used a very raw 18S phylogeny of Craniates to introduce phylogeny to 
students, and I would like to estimate bootstrap or likelihood values 
for branches. Sorry for this long message, but I hope you can answer at 
least some of my questions.

1) For bootstrapping, I obtain "zero" values for some of them and wonder 
: i) if it is possible (and how to interpret it) ; ii) what to change to 
correct it ?
Here is the script (the "alnx.fasta" file can be found at the end of 
this message) :

library(ape)
alnx2 <- read.dna(file = "alnx.fasta", format = "fasta")
alnxdist <- dist.dna(alnx2, model = "raw", pairwise.deletion = FALSE)
trx <- nj(alnxdist)
rtrx <- root(trx, "Branchiostoma")
plot(rtrx)

bp <- boot.phylo(rtrx, alnx2, function(x) nj(dist.dna(x, model = "raw", 
pairwise.deletion = FALSE))) # I also obtain zero values if 
pairwise.deletion = TRUE
nodelabels(bp)


2) Secondly, I also would like to obtain likelihood values for branches 
(I think it is the second common kind of values found on branches, with 
bootstrap ones), but could not find a function to do so. Would you know 
one ?
If I try maximum likelihood estimation, are those likelihood values 
calculated for the branches ? I see them for trees and sites, but not 
for branches…

library(phangorn)
alnx2pml <- pml(rtrx, as.phyDat(alnx2))
alnx2pmloptim <- optim.pml(alnx2pml) # This is just a test ; I don't 
really need a model
plot(alnx2pmloptim)
#The following commands do not seem to be a great idea (for boostrap) ; 
my computer doesn't like them…
# bp2 <- boot.phylo(rtrx, alnx2, function(x) optim.pml( pml( 
nj(dist.dna(x)) , as.phyDat(x)) ) )
# nodelabels(bp2)


3) Then, where to find likelihood values after a mrbayes run ?

library(phyloch)
mrbayes(alnx2, path = getwd(),ngen = 100, file = "test.con", run = 
FALSE) # I obtain the file I can use then in mrbayes


4) Eventually, for parsimony, what do the parsimony score represent ? Is 
it a way to weight it ? I suppose the answer is no, and parsimony scores 
are only there to compare them, not to deduce what is a "good" or "bad" 
score…

alnx2pars <- parsimony(rtrx, as.phyDat(alnx2))
alnx2parsoptim <- optim.parsimony(rtrx, as.phyDat(alnx2))
plot(alnx2parsoptim)


Thanks a lot in advance for your answer.
All the best,


Gwennaël Bataille

___________________________________________________________________________________________


 >Salmo
--------------------------------------------aagccatgcaagtctaagtaca--------------------cacggcc-ggtacagtgaaactgcgaatggctcattaaatcagttatggttcctttgatcgctccaac-gt--tacttggataactgtggcaattctagagctaatacatgcagacga-gcgctgacc-----------------------------tccggggatgcgtgcatttatcag-acccaaa-----------acc---catgcgggccaa---------------------------------tctcggttgc----cccggccgctt--------tggtgactctagataacctcg--agccgatcgcgcgccctttgtggcggtgacgtctcattcgaatgtctgccctatcaactttcgatggtactttctgtgcctaccatggtgaccacgggtaacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----tcggggaggtagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagtacactttaaatccttta-acgaggatccattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtatcttaaagttgctgcagttaaaaagctcgtagttggatctcgggatcgagctggcgg------tccgccgc----gaggcgagctaccgcctgtc-ccagcccctgcc--------tctcggcgccccctcga-tgctcttaactg-agtgtcccgc--ggggtccgaagcgtttactttgaaaaaattagagtgttcaaagcaggcccggtcg--cctgaataccgcagctaggaataatggaataggactccggt-tctattttgtgggtttttcttctgaac-tggggccatgattaagagggacggccgggggcattcgtattgtgccgctagaggtgaaattcttggaccggcgcaagacggacgaaagcgaaagcatttgccaagaatgttttcattaatcaagaacgaaagtcggaggttcgaagacgatcaga-taccgtcgtagttccgaccataaacgatgccaactagcgatccggcggcgtt-attcccatgacccgccgggcagc-gtccgggaaaccaa-agtctttgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacgggaaacctcacccggcccggacacggaaaggattgacagattgatagctctttctcgattctgtgggtggtggtgcatggccgttcttagttggtggagcgatttgtctggttaattccgataacgaacgagactccggcatgctaactagttatgcggccccg--agcggtcggcgt-ccaacttcttagagggacaagtggcgttcagccacacgagattgagcaataacaggtctgtgatgcccttagatgtccggggctgcacgcgcgccacactgagcggatcagcgtgtgtct-acccttcgccgagaggcgtgggtaacccgctgaaccccactcgtgatagggattggggattgcaattatttcccatgaacgaggaattcccagtaagcgcgggtcataagctcgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgattggatggtttagtgaggtcctcggatcggccctgccgagg-tcggtcacggccc-tggtggagcgccgagaagacgatcaaacttgactatctagaggaagtaaaagt-------------------
 >Bufo
--------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagccatgcacgtgtaagtacgcacggcc-ggtacagtgaaactgcgaatggcnnnnnnnnnnnnnnnnnnnnnnnnnnatcgctccaaccgt--tacttggataactgtggtaattctagagctaatacatgccgacga-gcgctgacc-----------------------------cccagggatgcgtgcatttatcag-accaaaa-ccaatcggggnnngggcgcncgggncnnggnntngggggtggtctnggcctcccnncncagccncnncngctctcccnngncgctt--------tggtgactctagataacctcg--ggccgatcgcacgtcccc-gtgacggcgacgatccattcggatgtctgccctatcaactttcgatggtactttctgcgcctaccatggtgaccacgggtaacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaagganggcagcaggcgcncanattacccactcccgac----ncggggagntagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagtacactttaaatccttta-acgagganctattggagggcnagtctggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtatattaaagttgctgcagttnnaaagctcgtagnnngatcttgggatcgagctng--g------tccgccgc----gaggcga-cnnccgccngtc-ccagcccccg----------tctcggcgcctcccnna-tgctcttgactg-agtgtcccg---gggncccgaannnnntactttgaaaaaattagagtgttcaaagcaggccgggtcg--cctgaatacttcagctaggaataatggaataggactccggt-tctattttgttggttt----tcggaac-tggggccatgattaagagggacgnnnnnnnn-atccgtattgcgccgctagaggtnaaattcttggaccggcgcnagacgaaccaaagcgaaagcatttgccaagaatgttttcattaatcaagnangaaagtcggaggttcgaagacgatcaga-taccgtcgtagttccgaccataaacgatgccgaccggnnatccggnggnntt-attcccatgacccgccgagcagc-ttccgggaaaccaa-agtctttgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtg--gcaggcggcttnatttnnnnnaacacgggaaacctcacccggcccggacacggaaaggatngacagattgatagctctttctcgattctgtgggnnnnnntgcatggcnnnncttagttggtggagcnatttgtctngttnattccgataacgaatgagactnctccatgctnactagttacgcgaccccn--nnnnntccgcgt-ccaacttcttagagggacaagtggngttcagccacgcgagatcgagcaataacaagtctgtgatgcccttagatgtccnnnncttcacnngcgctncactnaacggaccagcgtgtgtct-acccttcgccgacaggtcggggtnacccgctgaaccccgttcgtgatagggatcggggattgcaattatttcccatgaacgaggaattcccagtaagtgcgggtcataagctcgcgttgattnngtccctnccctttgtacacaccgcnnntcgctactaccgattggatggtttagtgaggtcctcggatcggccccgccgggg-ncggcgacggccc-nnnngnagcgccgagaagacgatcaaactnnactatctagaggaag--------------------------
 >Crocodylus
---------------------agcatatgcttgtctcaaagattaagccatgcatgtctaagtaca--------------------cacggcc-ggtacagtgaaactgcgaatggctcattaaatcagttatggttcctttggtcgctccaaccgt--tacttggataactgtggtaattctagagctaatacatgccgacga-gcgccgacc-----------------------------tccggggacgcgtgcatttatcag-accaaaa-ccaa--------------cccgg-------------g--------------cccgcc--------------------cggccgctt--------tggtgactctagataacctcg--agccgatcgcacgccccc-gcggcggcgacgacccattcgaatgtctgccctatcaactttcgatggtactgtctgtgcctaccatggtgaccacgggtgacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----ccggggaggtagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagcgcactttaaatccttga-gcgaggatccattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtatcttaaagttgctgcagttaaaaagctcgtagttggatcttgggatcgagctggcgg------tccgccgc----gaggcgagccaccgcctgtc-ccagcccctgcc--------tctcggcgcccccttga-tgctcttagctg-agtgtcccgc--ggggcccgaagcgtttactttgaaaaaattagagtgttcaaagcaggcc-ggccg--ccggaatactccagctaggaataatggaataggactccggt-tctattttgttggttt----tcggaac-tggggccatgattaagagggacggccgggggcattcgtattgtgccgctagaggtgaaattcttggaccggcgcaagacggaccaaagcgaaa-catttgccaagaatgttttcattaatcaagaacgaaagtcggaggttcgaagacgatcaga-taccgtcgtagttccgaccataaacgatgccgactagcgatccggcggcgtt-attcccatgacccgccgggcagc-ttccgggaaaccaa-agtctttgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacgggaaacctcacccggcccggacacggaaaggattgacagattgatagctctttctcgattctgtgggtggtggtgcatggccgttcttagttggtggagcgatttgtctggttaattccgataacgaacgagactctggcatgctaactagttatgcgaccccc-gagcggtcggcgt-ccaacttcttagagggacaagtggcgttcagccacccgagattgagcaataacaggtctgtgatgcccttagatgtccggggctgcacgcgcgctacactgactggctcagcgtgtgtct-accctacgccgacaggtgcgggtaacccgttgaaccccattcgtgatggggatcggggattgcaattattccccatgaacgaggaattcccagtaagtgcgggtcataagctcgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgattggatggtttagtgaggtcctcggatcggccccgccgggg-tcggtcacggccc-tggcggagcgccgagaagacggtcgaacttgactatctagaggaagtaaaagtcgtaacaaggtttccgtag
 >Ornithorhynchus
---------------------agcatatgcttgtctcaaagattaagccatgcatgtctaagtaca--------------------cacggcc-ggcacagtgaaactgcgaatggctcattaaatcagttatggttcctttggtcgctcgctccctcctacttggataactgtggtaattctagagctaatacatgccgacga-gcgctgacccgggcccctttccccccgtgggtgggggctccggggatgcgtgcatttatcag-accaaaa-ccaa--------------cccggcggtttccccccaa--------------ccccccaaccaggggcgggggtgccccggccgctt--------tggtgactctagataacctcg--ggccgatcgcacgccccccgtggcggcgatgacccattcgaacgtctgccctatcaactttcgatggtacttgccgtgcctaccatggtgaccacgggtgacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----ccggggaggtagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagcacactttaaatccttttcgcgaggatccattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtatcttaaagttgctgcagttaaaaagctcgtagttggatcttgggatcgagctggcgg------tccgccgc----gaggcgagccaccgcctgtc-cccgcccctgccc-------tctcggcgccccctcga-tgctcttagctg-agtgtcccgc--ggggcccgaagcgtttactttgaaaaaattagagtgttcaaagcaggcccggtcg--cctggatactccagctaggaatgatggaataggaccccggtgcctattttgttggttt----tcggaac-tggggccatgattaagagggacggccgggggcattcgtattgtgccgctagaggtgaaattcttggaccggcgcaagacggaccagagcgaaagcatttgccaagaatgttttcattaatcaagaacgaaagtcggaggttcgaagacgatcaga-taccgtcgtagttccgaccataaacgatgccgactcgcgatccggcggcgtt-attcccatgacccgccgggcagccttccgggaaaccaa-agtctttgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacgggaaacctcacccggcccggacacggaaaggattgacagatcgatagctctttctcgattctgtgggtggtggtgcatggccgttcttagttggtggagcgatttgtctggttaattccgataacgaacgagactctgacatgctaactagttacgcgaccccccgagcggtcggcgt-ccaacttcttagagggacaagtggcgtttagccacccgagattgagcaataacaggtctgtgatgcccttagatgtccggggctgcacgcgcgctacactgactggctcagcgtgtgtct-accctccgccgacaggtgcgggtaacccgttgaaccccattcgtgatggggatcggggattgcaattattccccatgaacgaggaattcccagtaagtgcgggtcataagcttgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgattggatggtttagtgaggtcctcggatcggccccgccgggggtcggccacggcccctggcggagcgctgagaagacggtcgaacttgactatctagaggaagtaaaagtcgtaacaaggtttccgtag
 >Gallus
-----------------------------------------attaagccatgcatgtctaagtaca--------------------cacgggc-ggtacagtgaaactgcgaatggctcattaaatcagttatggttcctttggtcgctcccctcccgttacttggataactgtggtaattctagagctaatacatgccgacga-gcgccgacc-----------------------------tccggggacgcgtgcatttatcag-accaaaa-ccaa--------------cccgg-------------g--------------ctcgcc--------------------cggcggctt--------tggtgactctagataacctcg--agccgatcgcacgccccc-gtggcggcgacgacccattcgaatgtctgccctatcaactttcgatggtactgtctgtgcctaccatggtgaccacgggtaacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----ccggggaggtagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagtccactttaaatccttta-acgaggatccattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtatattaaagttgctgcagttaaaaagctcgtagttggatcttgggatcgagctggcgg------tccgccgc----gaggcgagctaccgcctgtc-ccagcccctgtc--------tctcggcgccccctcga-tgctcttaactg-agtgtcccgc--ggggcccgaagcgtttactttgaaaaaattagagtgttcaaagcaggct-ggccg--ccggaatactccagctaggaataatggaataggactccggt-tctattttgttggttt----tcggaaa-cggggccatgattaagagggacggccgggggcattcgtattgtgccgctagaggtgaaattcttggaccggcgcaagacgaactaaagcgaaagcatttgccaagaatgttttcattaatcaagaacgaaagtcggaggttcgaagacgatcaga-taccgtcgtagttccgaccataaacgatgccgactcgcgatccggcggcgtt-attcccatgacccgccgggcagc-tcccgggaaaccca-agtctttgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacgggaaacctcacccggcccggacacggacaggattgacagattgagagctctttctcgattccgtgggtggtggtgcatggccgttcttagttggtggagcgatttgtctggttaattccgataacgaacgagactctggcatgctaactagttacgcgaccccc-gagcggtcggcgt-ccaacttcttagagggacaagtggcgttcagccacccgagattgagcaataacaggtctgtgatgcccttagatgtccggggctgcacgcgcgctacactgactggctcagcttgtgtct-accctacgccggcaggcgcgggtaacccgttgaaccccattcgtgatggggatcggggattgcaattattccccatgaacgaggaattcccagtaagtgcgggtcataagctcgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgattggatggtttagtgaggtcctcggatcggccccggcgggg-tcggccacggccc-tgccggagcgtcgagaagacggtcgaacttgactatctagaggaagtaaa----------------------
 >Squalus
---------------------agcatatgcttgtctcaaagattaagccatgcatgtctaagtaca--------------------cacggcc-ggtacagtgaaactgcgaatggctcattaaatcagttatggttcctttgatcgctccaaacgt--tacttggataactgtggtaattctagagctaatacatgccaacga-gcgctgacc-----------------------------ctctgggatgcgtgcatttatcag-accaaaa-ccaa--------------tc-ggg---------------------------cttgcc--------------------cggcagctt--------tggtgactctagataacctcg--ggctgatcgcacgtcctc-gtgacggcgacgactcattcgaatgtctgccctatcaactatcgatggtactttctgtgcctaccatggtgaccacgggtaacggggaatcagggttcgattccggagagggagcctgagaaacagctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----tcggggaggtagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagtacactttaaatccttta-acgaggaactattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtacattaaagctgctgcagttaaaaagctcgtagttggatcttgggatcgagctggcgg------tccgccgc----gaggcgagctaccgcctgtc-ccagcccctgcc--------tctcggcgctcccttga-tgctcttagctg-agtgtcctg---ggggtccgaagcgtttactttgaaaaaattagagtgttcaaagcaggcc-ggtcg--cctgaatactccagctaggaataatggaataggaccccggt-tctattttgttggttt----tcggaac-tggggccatgattaagagggacggccgggggcattcgtattgtgccgctagaggtgaaattcttggaccggcgcaagacgaacaaaagcgaaagcatttgccaagaatgttttcattaatcaagaacgaaagtcggaggttcgaagacgatcaga-taccgtcgtagttccgaccataaacgatgccaactagcgatccggcggcgtt-attcccatgacccgccgagcagc-ttccgggaaaccaa-agtctttgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacgggaaacctcacccggcccggacacggaaaggattgacagattgatagctctttctcgattctgtgggtggtggtgcatggccgttcttagttggtggagcgatttgtctggttaattccgataacgaacgagactcctccatgctaaatagttacgcgaccccc-gagcggtccgcgt-ccaacttcttagagggacaagtggcgtatagccacacgagattgagcaataacaggtctgtgatgcccttagatgtccggggctgcacgcgcgctacactgaatggatcagcgtgtgtct-accctacgccgccaggtgtgggtaacccgttgaaccccattcgtgatggggattgggaattgcaattatttcccatgaacgaggaattcccagtgagtgcaggtcataagctcgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgattggatggtttagtgaggtcctcggatcggccccgccggag-tcggcaacggccc-tggcggagcgccgagaagacgatcaaacttgactatctagaggaagtaaaagtcgtaacaaggtttcc----
 >Latimeria
tacctggttgatcctgccagtagcatatgcttgtctcaaagattaagccatgcatgtctaagtaca--------------------aacggtg-cgtacagtgaaactgcgaatggctcattaaatcagttatggttcctttgatcgctccaa-cgt--tactcggataactgtggtaattctagagctaatacatgccgacga-gcgctgacc-----------------------------ttcggggatgcgtgcatttatcag-accaaaa-ccaa--------------tccggg---------------------------tccgcc--------------------cggccgctt--------tggtgactctagataacctcg--ggccgatcgcacgtcctc-gtggcggcgacgattccttcgaatgtctgccctatcaactttcgatggtactttctgtgcctaccatggtgaccacgggtaacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----gcggggaggtagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagtacactttaaatccttta-acgaggatctattggagggcaagtctggtgccagcagccgcggtaattccagctccagtagcgtatattaaagttgctgcagttaaaaagctcgtagttggatcttgggatcgagctggcgg------tccgccgc----gaggcgagctaccgcctgtc-ccagcccctgcc--------tcttggcgctcccttga-tgctcttaactg-agtgtcctg---ggggtccgaagcgtttactttgaaaaaattagagtgttcaaagcaggcc-ggtcg--cttggatacttcagctaggaataatggaataggactccggt-tctattttgttggttt----tcggaac-tggggccatgattaagagggacggccgggggcattcgtattgtgccgctagaggtgaaattcttggaccggcgcaagacggacaaaagcgaaagcatttgccaagaatgttttcattaatcaagaacgaaagtcggaggttcgaagacgatcaga-taccgtcgtagttccgaccataaacgatgccaactaccgatccggcggcgtt-atttccatgacccgccgggcagg-ttccgggaaaccaa-agtctttgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacgggaaacctcacccggcccggacacggaaaggattgacagattgatagctctttctcgattctgtgggtggtggtgcatggccgttcttagttggtggagcgatttgtctggttaattccgataacgaacgagactcctccatgctaaatagttacgcgacccc--gagtggtcggcgt-ccaacttcttagagggacaagtgacgtttagccacacgagattgagcaataacaggtctgtgatgcccttagatgtccggggctgcacgcgcgctacactgaatggatcagcgtgtgtct-accctacaccgacaggtgcgggtaacccgttgaaccccattcgtgatagggatcggggattgcaattatttcccgtgaacgaggaattcccagtaagtgcgggtcataagctcgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgattggatggtttagtgaggtcctcggatcggacccgccgggg-tcgtccgcggccc-tggcggagcgctgagaagacgatcaaacttgactatctagaggaagtaaaagtcgt----------------
 >Lampetra
nacctggttgatcctgccagtagcatatgcttgtctcaaagattaagccatgcatgtctgcgtgca--------------------aacggat-gttacagtgaaactgcgaatggctcattaaatcagttatggttcctttgatcgctc-gaccgt--tgcttggataactgtggtaattctagagctaatacatgctgacga-gcgctgacc-----------------------------tccggggatgcgtgcacttattag-accaaaa-ccaa--------------tccggg---------------------------cttgcc--------------------cggacgctt--------tggtgactctggataaccacgtgggcagatcgcacggccctggtgctggcgacgtatctttcgaatgtctgccctatcaacttacgatggcaggctccgtgcctaccatggtgaccacgggtaacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----tcggggaggtagtgacgaaaaataacaatacaggactctttcgaggccctgtaattggaatgagtacactttaaatccttta-acgaggatccattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtatattaaagctgttgcagttaaaaagctcgtagttggatcttgggaaggggcttgcgg------tccgccgc----gaggtgtgtcactgcctgtc-ccggcccccacc--------tctcggtgctccccgga-tgctcttggttg-agtgtcctgtg-ggggtccgaagcgtttactttgagaaaattggagtgttcaaagcaggcc-gcacg--cctgaacagtgcagctgggaataatggaataggacctcggt-tctattttgttggttt----tcggaac-ggaggccatgattaagagggactgccgggggcattcgtattgtgccgttagaggtgaaattcttggatcggcgcaagacgagcgaaagcgaaagcatttgccaagaatgtcttcattaatcaagaacgaaagtcggaggttcgaaggcgatcaga-taccgccctagttccgaccataaacgatgccaactggcgatcaggcggcgtt-attcccatgacctgcctggcagc-ttgcgggaaaccaa-agtgtttgggttccgggggaagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacgggaaaactcacccggcccggacacggagaggattgacagattgagagctctttctcgattccgtgggtggtggtgcatggccgttcgtagttggtggagcgatttgtctggttcattccgataacgaacgagactccgacgtgctaactagctacgcggcccct-gtgcggtcggcgt-tgagcttcttagagggacgagtggctttcagccacacgagattgagcaataacaggtctgtgatgcccttagatgtccggggccgcacgcgcgctacactgaatggatcagcgtgtgtcc-gcccttcgccggcaggcgtgggtaacccgttgaaacccattcgtgatagggattggggattggaactgttccccatgaacgaggaattcccagtaagcgcgagtcataagcttgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgattggatggtttagtgaggtcctcggattggccccgctgggg-caggcgactgccc-tgggggtgcgctgagaagacgatcgaacttgactgtctagaggaagtaaaagtcgt----------------
 >Myxine
nccctggttgatcctgccagccgcatatgcttgtctcaaagactaagccatgcatgtctaagtgcg--------------------aacggacagacccgttgagactgcgaatggctcattaaatcagttatggtctctttgagcgctcgga-cgt--tacttggataactgtggcaattctagagctaatacatgcaaacga-gcgccggtccccgcgggtgtcgggttctcctggcgtcctgtggggaggcgcgcatttatcagcaccaaaaatcga--------------cgcggcg--------------------------cccacg--------------------cgggcccgtccacgggatggtgactctggataa--acgattgcagatcgctcggcctccgcgccggcgacgtttcattcgaatgtctgccctatcaactttcgatggcaggcttcgcgcctgccatggtggctacgggtgacggggaatcagggttcgattccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----acggtgaggtagtgacgaaaaataccgatgcaggcctcggtcgaggcgctgctatcggaatgggtgcaccttaaacccatgt-gcgaggatccattggagggcaagtctggtgccagcagccgcggtaattccagctccaacagcgtaagcgaacgctgttgcagttaaaaagctcgtatttggaaatcacgccggggctcgcgggggggacgcgtcgc----aaggcgcgcttcctctccccgcccgtccccggcggcgagactgtcggagccctgcgga-cgctcttggatg-agtgtccgttg-tgggccgaaagcgtttaccttgaggaaactggagtgctcagagcgggtc-ggtagagcctgtacaccgcagctgggaataatggaatagggcctcggt-cctattttgttggtttt---gcgggac-ggaggtcatgattgagagggactgccgggggcattcgtactgcgccgcgagaggtgaaattctgggaccggcgcaagacggactaaagcgaaagcatttgccaagaatgttttccttaatcaagaacgaaggtcggaggctcgaaggcgatcaga-taccgccctagtttcgacggtaaactatgccgaccggcgatcgggcggcgtcgaatggcatgacccgtccggcagccatgagggaaaccaggagtttctgggttccggggggagtatggttgcaaagctgaaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggctcaatttgactcaacacgggaaagctcacctgggccggacacgagaaggattgacagactgagagctctttcacgattctgtgggtggtggtgcatggccgttcttagttggtggagcgatccgtctggttgattccgataacgagcgagactccgacacgctaactagttccgcgaccctg-gtgtggccggcggactaacttcttagagggacgagcggctgcaagccgtgcgagatggagcaataacaggtctgtgatgcccttcgatgtccggggccgcacgcgcgctacactggacgggccagcgtgtaccttgcccttcgccgtcaggctcgggtaaaccgctgagccccgtccgtgatggggactggggcttgagacagtgtcccacgaacgaggaattcccagtaagcgcgagtcatcagctcgcgttgattaagtccctgccctttgtacacaccgcccgtcgctactaccgatcggacggtttggtgagatcctcggatcagcccctgcacgggccgttctcggctcgtgccggtgcgccgaaaagatgagcgaacttgactgtctagaggaagtaaaagtcgt----------------
 >Branchiostoma
--------------------------------------------aagccatgcacgtgcaagttta--------------------aactgtc----ccagtgaaactgcgaatggctcattaaatcagttatggttcctttgatcg-tcacatcct---acatggataactgtggtaattctagagctaatacatgcggaagaagcgccgacct----------------------------cacggtctggcgtgcatttatcag-accaaga-ccga--------------cccgggg--------------------------ttcgcc-------------------ccggtccctt--------tggtgactctggataacc-ca---gccgatcgcacggtcttcgcaccggcgacagatcattcgaatgtctgccctatcaactttcgatggtaggttctgtgcctaccatggtggcaacgggtgacggggaatcagggttcggttccggagagggagcctgagaaacggctaccacatccaaggaaggcagcaggcgcgcaaattacccactcccgac----tcggggaggtagtgacgaaaaataacaatacgggactctttcgaggccccgtaattggaatgggtacactttaaatccttta-acgaggatctattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtatattaaagttgttgcggttaaaaagctcgtagttggatcttgggaccgggcttgcgg------tccgccgc----gaggcgtgtcactgctcgtc-ccggccctcccc---------gccggattctccttgg-tgctcttaactg-agtgcctcg---gggtgccggagcgtttactttgaaaaaattagagtgttcaaagcaggcctgg-cg--cctgaatagtggtgcatggaataatggaataggacctcggt-tctatttcgttggttt----tcggaacgtgaggtaatgatcaagagggacggacgggggcattcgtattgcggcgggagaggtgaaattcttggatcgccgcaagacgaaccactgcgaaagcatttgccaagaatgttttcattgatcaagaacgaaagttgtgggcgcgaaggcgatcaga-taccgccctagtcacaaccataaacgatgccaaccagcgatccgccggcgtt-acttcgatgacccgatgggcagc-tcccgggaaacctg-agttttcgggttccgggggaagtatggttgcaaagctggaacttaaaggaattgacggaagggcaccaccaggagtggagcctgcggcttaatttgactcaacacggggaaactcacccggcccggacacagtaaggattgacagattgagagctctttcttgattctgtgggtggtggtgcatggccgttcttagttggtggagcgatttgtctggctaatcccgataacgaacgagactctggcatgctaactagttcggcgatcccg--cgcgatcggccg--caacttcttagagggacagccggcagtaagccggacgagatggagcaataacaggtctgtgatgcccttagatgtccggggccgcacgcgcgctacaatgaaggcatcagcgagtctttcgcc-ttcgccgaaaggtgcgggtaacctgctgaaccgccttcgtgctagggatcggggattgcaattatctcccatgaacgaggaattcccagtagatgcgtgtcatcagcgcgcgttgattacgtccctgccctttgtacacaccgcccgtcgctactaccgattgaatggtttagtgaggccagtcgatcggcccctctcggg-ccggcaacggtc--tggaggagcgccgagaagccgatcaaacttgaccatttaaaggaa---------------------------
 >Cerastes
-----------------------------------------------ccatgcacgtctaagtata--------------------aacagaa--atacagtaaaactgcaaatggctcattacaacagttatagtttctttgataac---aaacgt-ttacatggataaccgtggtaattctagagctaatacatgagcacat--tctcaactg----------------------------ttttagaagagaagcatttattag-ataaaaaaccaa--------------tatatgtt-------------------------tttaaaa-------------------cataaaagt--------tggtgatttacaataactaag----caaatcgcacagtgc--aaactggcgataaatcattcaagtttctgacctatcagctttcgacggtaaggtattggcttaccgtggcagtgacggttaacggggaattagggttcaattccggagagggagcctgagaaacggctaccacatctaaggaaggcagcaggcgcgcaaattacccaattctaacagcataagagaggtagtgacaagaaataacagtacaaggcagttaaaatgctttgtaattggaatgatagaaatttaaatacttttta-aagtatcaattggagggcaagtctggtgccagcagccgcggtaattccagctccaatagcgtatattaaaattgttgcagttaaaaagctcgtagttgaatttt-tgctaaaaataaccgg-----tctgcttttattaataaaagtggtatcttggt--gtgtttttagc---------aataatgtcctttgaaatgttttttactttattgtaaaaagcaattttcaggatttttactttgagaaaattagagtgtttcaagcaggct--aacgt-tttgaatactgcagcatggaataataaaataggattttagt-tctacgttattggttt----taagaac-taaattaatgattgataggagcagttgggggcatttgtatttaactgtcagaggtgaaattcttagatttgttaaagacacactactgcgaaagcatttgccaaga-tgt-ttcattaatcaagaacgaaagtaaggggatcgaagacgatcagaataccgtcgtagtcttaactataa-ctatgccgactaga----------------------------------------------------------------------------------------------------------taatgga-----------------------------------------------------------------------------------------------------------------------------ggtcgtcctta-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


-- 
Gwennaël BATAILLE, PhD student - Teaching assistant

Earth and Life Institute
Université Catholique de Louvain
SST/ELI/ELIB
Bâtiment Carnoy
Croix du sud 4-5, bte L7.07.04
1348 Louvain-la-Neuve
BELGIUM



More information about the R-sig-phylo mailing list