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Alignments, gaps and phylogeny

Joe Felsenstein joe at evolution.genetics.washington.edu
Fri Jul 5 12:12:41 EST 1996

In article <4rj9f8$cp5 at freenet-news.carleton.ca>,
Robert J. Forster <ac562 at FreeNet.Carleton.CA> wrote:
>After reading the phylip manual I decided to use dnaml to derive the
>distances and to reconstruct phylogenetic trees.  I trimmed the 5' and 3'
>ends so that most of the sequences start and end in nearly the same
>places.  I would like to include in the analysis the genbank sequence
>which has about 250 bp missing near its 3' end.  Do I need to trim all the
>sequences back to this point?

No. In PHYLIP in the DnaML program, gaps are treated as unknown nucleotides
(equivalent to "?").  You do not need to trim, and might even gain a little
information by leaving those areas in, as long as you think the alignment
is good there.

>the important information was held.  Some researchers eliminate regions
>due to length variations in the sequences, others restrict their analysis
>to sequences which have 90% of the sequence available, whilst others
>eliminate all sequence which cannot be aligned without gaps (my choice of
>an outgroup species for a root would certainly eliminate a fair bit of
>sequence using this option!).  

None of these practices are necessary.

>What to do, what to do?  I've tried a few different methods and
>yes I get slightly different trees with each method. Does the J-K distance
>method require gaps to be removed?


Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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