Err.: one or more missing sequences in block 2

[Quentin CAUDRON]

Hello,

I am trying to construct a phylogenetic tree using the output from Clustal Omega. When I write a PHYLIP file from ClustalO, it cannot be read by PhyML - I get,

Err.: one or more missing sequences in block 2

When this alignment file is created in SeaView instead, PhyML has no problem reconstructing the tree.

When you call "Align" in SeaView, it prints out the command that it uses. I've ensured I use the same options in my command-line call to ClustalO. The alignments look the same when rendered visually. The files differ in that my CLI-output file does not group the nucleotides in groups of ten, whereas the SeaView-output file does. Could this be the problem ?

I attach both files, in case you're able to spot the issue.

Thanks very much !

Quentin

[Yohannes Mehari]

Hi Quentin

Did you figure it out the error with clustal aligned sequence in PhyML. I am having the same problem. 

Thank you

yohannes

[Quentin CAUDRON]

It's been a while, but it's something about the formatting of whitespace in the file, if I recall. The simple solution was to open it in SeaView ( I think ? ) and save it as the same file type. I was then able to open the file with PhyML. Sorry this is somewhat vague - I haven't really played with these tools since.

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