Dear Gwennaël,
first it seems there was a bug in the function prop.clades from ape
introduced recently, results in many zeros of bootstrap values.
This function needs to be replaced in the ape package:
prop.clades <- function (phy, ..., part = NULL, rooted = FALSE)
{
if (is.null(part)) {
obj <- list(...)
if (length(obj) == 1 && class(obj[[1]]) != "phylo")
obj <- unlist(obj, recursive = FALSE)
part <- prop.part(obj, check.labels = TRUE)
}
bp <- prop.part(phy)
if (!rooted){
bp <- postprocess.prop.part(bp)
part <- postprocess.prop.part(part) # This line I added!!
}
n <- numeric(phy$Nnode)
for (i in seq_along(bp)) {
for (j in seq_along(part)) {
if (identical(bp[[i]], part[[j]])) {
n[i] <- attr(part, "number")[j]
done <- TRUE
break
}
}
}
n
}
On 3/12/12, Gwennaël Bataille <gwennael.batai...@uclouvain.be> wrote:
> 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…
The branch length in a ML tree are (proportional to) time (molecular
clock) or the expected number of substitutions per site.
>
> 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)
>
There is function for bootstrapping in phangorn:
library(phangorn)
alnx2pml <- pml(rtrx, as.phyDat(alnx2))
alnx2pmloptim <- optim.pml(alnx2pml, TRUE)
# some tree rearrangements, otherwise you may get some zeros
alnx2bs <- bootstrap.pml(alnx2pmloptim, optNni=TRUE)
plotBS(alnx2pmloptim$tree, alnx2bs)
>
> 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…
The parsimony score is the minimal number of substitutions needed to
account for the data on a phylogeny.
If you weigh a tree with the parsimony score the edge length represent
the minimal number of substitutions needed.
>
> alnx2pars <- parsimony(rtrx, as.phyDat(alnx2))
> alnx2parsoptim <- optim.parsimony(rtrx, as.phyDat(alnx2))
> plot(alnx2parsoptim)
pratchet is likely to find better tree (not for this small tree here)
alnx2pars <- parsimony(rtrx, as.phyDat(alnx2))
alnx2parsoptim <- pratchet(as.phyDat(alnx2), start=rtrx)
alnx2parsoptim <- acctran(alnx2parsoptim, as.phyDat(alnx2))
# assign edge length via ACCTRAN criterion,
# the assignment for the edge length is in general not unique!!!
tree <- midpoint(alnx2parsoptim) # midpoint rooting for a nicer look
plot(tree)
edgelabels(round(tree$edge.length, 3), adj = c(.5, 1), frame="none")
add.scale.bar()
>
>
> 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
>
> _______________________________________________
> R-sig-phylo mailing list
> R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
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