<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I’m sure it is, just a another case of reinventing the wheel taking less time than reading the manual….<div class=""><br class=""></div><div class=""><br class=""></div><div class="">Liam.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 11 May 2016, at 12:18 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" class="">cjfields@illinois.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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I think this functionality (mapping from long name to short PHYLIP-compatible and back) is in bioperl. Would have to dig it up but I recall support being added many moons ago.
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<div class="">chris</div>
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<div class="">On May 10, 2016, at 8:30 PM, Liam Elbourne <<a href="mailto:liam.elbourne@mq.edu.au" class="">liam.elbourne@mq.edu.au</a>> wrote:</div>
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I think it is 10 characters (sequence starts at character 11), not that two characters is worth quibbling about, I just map the original names to hex numbers (which I think is likely to cover the number of sequences one can realistically align…), and then swap
out the hex codes when I’ve finished with the alignment/tree etc, for what that is worth…
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<div class="">Liam.</div>
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<div class="">On 11 May 2016, at 9:00 AM, Torsten Seemann <<a href="mailto:torsten.seemann@infotech.monash.edu.au" class="">torsten.seemann@infotech.monash.edu.au</a>> wrote:</div>
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I only have a distance matrix derived from Mash and so I need a program to<br class="">
make a tree from distances. I do not think I can use RAxML or Mr. Bayes,<br class="">
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<div class="">The PHYLIP format can be used for distance matrices, and PHYLIP has various tools to build trees from them:</div>
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<div class=""><a href="http://evolution.genetics.washington.edu/phylip/progs.data.dist.html" class="">http://evolution.genetics.washington.edu/phylip/progs.data.dist.html</a><br class="">
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<div class="">The MASH dist output file is VERY close to being a valid .PHY file (If taxnames <= 8 chars) but Brian Ondov seems unwilling to implement it within MASH - see my issue here:
<a href="https://github.com/marbl/Mash/issues/9" class="">https://github.com/marbl/Mash/issues/9</a></div>
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<div class="">Torst</div>
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