Question: Is FastML a good server for reconstructing ancestral protein sequence?
3
gravatar for lia.elias
5.7 years ago by
lia.elias40
lia.elias40 wrote:

After a MSA using clustal, can I load the alignment in FASTA format to FastML to get a reliable ancestor protein sequence prediction?

ADD COMMENTlink modified 15 months ago by lhernanj0 • written 5.7 years ago by lia.elias40

Hello,

I have a question: how to calculate the difference in log-likelihood between the most likely ancestral sequence at node N1 and the 100th most likely sequence??

thanks in advance

laura

ADD REPLYlink written 15 months ago by lhernanj0
3
gravatar for JulianZ
5.6 years ago by
JulianZ70
Australia
JulianZ70 wrote:

Yes, you can use FastML to get reliable ancestor sequences. I should note that the previous steps leading to this need to be performed very carefully, i.e., your alignment and tree need to be constructed correctly. The REAP protocol is pretty good at discussing the steps involved (paywall).

FastML itself can be annoying to use. Occasionally the server will not work (for whatever reason) and at other times very minor formatting issues in your supplied alignment or tree will cause it to break (and the server won't always tell you what the issue is).

An alternative is CODEML in the PAML package...although this is incredibly difficult to use and the documentation is crap hard to interpret.

I can expand on the sequence of steps that I believe need to be taken for ASR (formatting tricks, programs to use, etc.) if required.

ADD COMMENTlink modified 5.4 years ago • written 5.6 years ago by JulianZ70

Thank you very much JulianZ...

I would like to get the sequence of steps if you can share. I am a beginner in the field.................

Thanks

ADD REPLYlink written 5.6 years ago by lia.elias40
2

ADD REPLYlink modified 7 months ago by RamRS27k • written 5.6 years ago by JulianZ70
1

Thank you very much JulianZ. I have a doubt regarding the output we receive from the FastML. How do we know what is N1, N2 etc? i.e., How is this numbering done with the nodes? Can you please clear my doubt ASAP?

ADD REPLYlink written 5.6 years ago by lia.elias40
1

N1 is the oldest ancestor. After that, all other internal nodes of the phylogenetic tree are labelled in order ....N2, N3...etc. N2 and N3 for example would be children of N1. Extant sequences should maintain their original labels. I believe FastML provides a newick tree in one of the output files with the ancestor labelling included...so plotting that should give you a more `visual' idea of how the nodes are labeled. 

ADD REPLYlink written 5.6 years ago by JulianZ70

Thank you very much JulianZ. Your inputs gave me an overall idea of ASR. I have tried it out for my sequences. I will get back if I have any more queries.

Thank you again

ADD REPLYlink written 5.6 years ago by lia.elias40

Hi

I have a few more doubts.... Which kind of output should we consider regarding FASTML? Is it joint reconstruction file or marginal construction with/without indels?? 

One more thing.......I have used an outgroup while making the tree. Will this interfere with the accurate ASR?

Please answer............................................

ADD REPLYlink written 5.5 years ago by lia.elias40
1

Hmm good question. Depends on what your ultimate goal is, but typically you will just use the joint reconstruction (If you read up on the theory on the difference between joint and marginal this will make more sense). The marginal reconstruction is useful if you want to compare against the joint and get a sense of what positions were difficult for Fastml to infer (at least I think so?)....e.g. a position in an ancestor could be 50% likely to be a 'G' and 50% likely a 'C', rather than 90% likely.

And yes, you are meant to use an outgroup (depending on what you are reconstructing). I forgot to mention that before.

ADD REPLYlink modified 5.4 years ago • written 5.5 years ago by JulianZ70

Thank you very much.

ADD REPLYlink written 5.5 years ago by lia.elias40
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