How To Get Phylogenetic Tree From Nei Genetic Distance
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0
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13.3 years ago
Nasser Ali • 0

I want to generate a rooted phylogram ( tree ) for Omani pepole when I have the Matrix of Nei Genetic Distance. I find quite difficult to get the results. Please help me to resolve this problem.

Pairwise Population Matrix of Nei Genetic Distance:
No. Samples    202                        
No. Pops.    7                        

IR    0.000    0.464    0.300    0.310    0.455    0.251    0.175
SM    0.464    0.000    0.235    0.400    0.478    0.264    0.246
BT    0.300    0.235    0.000    0.279    0.352    0.224    0.195
SH    0.310    0.400    0.279    0.000    0.130    0.190    0.161
JK    0.455    0.478    0.352    0.130    0.000    0.288    0.258
DH    0.251    0.264    0.224    0.190    0.288    0.000    0.138
MS    0.175    0.246    0.195    0.161    0.258    0.138    0.000
phylogenetics tree distance matrix • 4.1k views
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4
Entering edit mode
13.3 years ago

The distance format for the Phylip suite is a bit pedantic, first column needs to be exactly 10 character long ... etc, this below works (select the outgroup yourself):

7
IR        0.000 0.464 0.300 0.310 0.455 0.251 0.175
SM        0.464 0.000 0.235 0.400 0.478 0.264 0.246
BT        0.300 0.235 0.000 0.279 0.352 0.224 0.195
SH        0.310 0.400 0.279 0.000 0.130 0.190 0.161
JK        0.455 0.478 0.352 0.130 0.000 0.288 0.258
DH        0.251 0.264 0.224 0.190 0.288 0.000 0.138
MS        0.175 0.246 0.195 0.161 0.258 0.138 0.000

alt text

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@Istvan Albert How to increase the sequence name from 10 characters to longer? How can I get the source code of neighbor phylip?

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not sure if the limit still applies, that answer was made 9 years ago,

if it is then it is a tool limitation, it means the tool cannot read longer names, thus your sole option is to shorten your names to 10 characters.

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Thanks for your reply. I am new to this field, and I am wondering if similar task can be performed by other tools (I have my own distance matrix). But most of the tools do not have any uniform input format, which is a bit annoying for multiple analysis. :(

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