Problems with constraint tree names spelling

[Wayne Dawson]

Dear Will et al.

I am currently trying to construct a simple phylogeny of 18 plant species using phyloGenerator1. I'm using both rbcl and matk genes. When I get to the constraint method stage, I have problems. First, I chose the phylomatic version, and entered in a txt file of an unaged newick tree. Then I was prompted to enter a phylomatic format taxonomy, which I did. But then pG returned me back to the constraint method prompt. So I chose newick, as in your video, and this time gave a tree with branch lengths (using the previous newick tree from Phylomatic), obtained using bladj in phylocom. But then pG tells me:

"Constraint tree does *not* match the species names you've inputed - this is case sensitive. Please load another file."

I don't know why there would be a spelling mistake, as I used the very same species list to generate the taxonomy list, and then the constraint tree using Phylomatic.

Any ideas where I'm going wrong here? My species list is:

Centaurea_jacea
Cirsium_oleraceum
Pulicaria_dysenterica
Senecio_jacobaea
Taraxacum_officinale
Rumex_maritimus
Rumex_obtusifolius
Silene_alba
Silene_vulgaris
Salvia_pratensis
Plantago_lanceolata
Plantago_major
Agrostis_capillaris
Brachypodium_sylvaticum
Dactylis_glomerata
Deschampsia_cespitosa
Phleum_pratense
Verbascum_thapsus

Constraint tree:

((((Senecio_jacobaea:46.875000,Taraxacum_officinale:46.875000)asteraceae:46.875000,((Plantago_lanceolata:31.250000,Plantago_major:31.250000)Plantago:31.250000,(Verbascum_thapsus:31.250000,salvia_pratensis:31.250000):31.250000):31.250000):31.250000,((Rumex_maritimus:44.500000,Rumex_obtusifolius:44.500000)Rumex:44.500000,(Silene_alba:44.500000,Silene_vulgaris:44.500000)Silene:44.500000)caryophyllales:36.000000):36.000000,(Agrostis_capillaris:80.500000,Brachypodium_sylvaticum:80.500000,Dactylis_glomerata:80.500000,Deschampsia_cespitosa:80.500000,Phleum_pratense:80.500000)poaceae:80.500000)poales_to_asterales:1.000000;


Many thanks in advance!

Wayne Dawson (University of Konstanz)

[Will]

Hello,

Thanks for getting in touch and using the program.

I think the problem is that your species list doesn't match your constraint tree. When I run the following in R:

require(ape)

tree <- read.tree("~/Downloads/wayne_tree.tre")

species <- read.table("~/Desktop/wayne_species.txt", header=FALSE, as.is=TRUE)[,1]

setdiff(species, tree$tip.label)

[1] "Centaurea_jacea"       "Cirsium_oleraceum"     "Pulicaria_dysenterica"

[4] "Salvia_pratensis"

...you can see that there are four species in your species list that aren't in your constraint tree.

Try again with a constraint tree that contains all of the species you are trying to build a phylogeny for. There's an example in the "Silwood plants" folder that comes with pG if you're having trouble.

I hope that helps, let me know if you run into any more difficulties,

Will

---

Need a phylogeny? Try phyloGenerator

Measuring phylogenetic structure? Try install.packages('pez')

Want something to read? Try PEGE journal club or willeerd

Will Pearse
Post-doc, ecology / evolutionary biology
Davies and Peres-Neto labs
Skype: will.pearse
Cell: (+1) 514-973-1987

[Wayne Dawson]

Darn, knew it would have been something simple and silly. Thanks Will, I should have spotted that error myself. I had already looked at the Silwood plants example, thanks for providing it.

However, now I have a new problem. The constraint tree loaded, and then I proceeded to use raxml, and specificied 1000 integrated bootstrap iterations. Then I wanted to apply rate smoothing, by typing 'pathd8', but then a system Error box appeared for PATHd8.exe, stating:

"The program can't start because cygwin1.dll is missing from your computer. Try reinstalling the program to fix this problem."

If I then proceed without rate smoothing, I get the same system error after specifying an outgroup.

I only downloaded and installed pG today,  any ideas why cygwin1.dll is missing?

Many thanks (again)

Wayne

[Will]

Hello,

I'm not quite sure why you were asked for an outgroup if you weren't rate-smoothing; I might take a look later to see if I've messed up a check somewhere in the code.

Can I just check; have you followed the instruction pG gives you at the rate-smoothing prompt:

PATHd8 requires 'cygwin' to be installed, and you don't have it.

website' - open cygwin website (so you can install it)

dll' - download Cygwin1.dll - copy this into the 'requires' folder inside your phyloGenerator distribution if installing Cygwin doesn't work for you

...and have you followed the instructions on the FAQ on the website?:

I can't get PATHd8 to work on a PC!

First, try installing Cygwin (type 'cygwin' when prompted to go to their website). If that doesn't work, you can try copying a DLL into the 'requires' folder inside the 'phyloGenerator' folder on your computer - again, you can download this when prompted too. If that doesn't work, please contact me. Those two steps have worked for everyone so far, but if they don't for you I want to know!

...if you have, then could you please try double-check that you've followed the installation instructions here (https://cygwin.com/install.html), and then copy-paste the exact error messages that you get from pG along with your operating system version etc.?

Thanks! Nearly there :D

Will

---

Need a phylogeny? Try phyloGenerator

Measuring phylogenetic structure? Try install.packages('pez')

Want something to read? Try PEGE journal club or willeerd

Will Pearse
Post-doc, ecology / evolutionary biology
Davies and Peres-Neto labs
Skype: will.pearse
Cell: (+1) 514-973-1987

[Wayne Dawson]

Hi Will,

I get no instruction given by pG at the rate-smoothing prompt, as you described.

I looked at the instructions on how to install Cygwin, installed it, and copied cygwin1.dll from my C:\cygwin\bin folder to the pG 'requires' folder.

Now pathd8 works fine and I have my tree!

Many thanks for your help, looking forward to building some bigger trees using pG in future.

Wayne

[Will]

Glad it's working! Fingers crossed for bigger trees :D

Will

---

Need a phylogeny? Try phyloGenerator

Measuring phylogenetic structure? Try install.packages('pez')

Want something to read? Try PEGE journal club or willeerd

Will Pearse
Post-doc, ecology / evolutionary biology
Davies and Peres-Neto labs
Skype: will.pearse
Cell: (+1) 514-973-1987