Bootstrapping in Neighbor (Phylip package)

[nehaverma]

Hi,

I am very new to phylogenetics. I have to construct Phylogenetic tree from SNP Golden Gate data. I generated distance matrix and used "Neighbor" of Phylip package. I am not sure how do I use bootstrapping there? Do I really need to do bootstrapping or the tree generated as it is I can use.trust.

Thanks
Neha

[cascoamarillo]

Wow. I have to take pieces of memmory I though they would be lost!

Once you have dist-neighbor analysis, reuse your initial dataset as input for bootseq (bootstrap/jacknife), do the boostraping and then use that output for dnadist-neighbor-consense. So basically you will have x (# bootstraps) alignments, x distance matrix, x trees.
....more or less

[cascoamarillo]

and remember to use the Multiple data sets option (M) to analyze them all