From genesup from gmail.com Mon Jun 9 08:20:48 2008 From: genesup from gmail.com (DimitryASuplatov) Date: Mon Jun 9 08:04:07 2008 Subject: [Molecular-evolution] Bootstrap interpretation Message-ID: <1213017648.14277.19.camel@linux-6n66.site> Hello, I want to generate "random" alignment to use it as a neutral evolution model for hypothesis testing. I need a phylogenetic tree of my species for that. I have used phylip package to generate a set of 1000 replicates, then I have used PMB model to calculate the distances with protdist and finally appllied neighbor and consese with default settings. As a result a have an unrooted tree with bootstrap values generaly better at the tips than in the center of the tree. In my understanding this is a normal case, though some values are equal to 25%. So my question is what could I do with this tree? As I understand, 25% values emphasize the fact that different parts of distant sequnces do not show consistency with overall comparison. I can not crop the alignment. Should I use neighbor-joining to calculate the tree directly from the alignment? Thanks. P.S. I have investigated 43 sequences with average length of 800 aa. The consese tree is included. +--------------------------------------------------------------------------------------------------------A4CHA4|A4C | | +------A5V4S1|A5V | +---------------------364.0-| | | +------Q8VQG6|Q8V | | | | +------Q83YY8|Q83 | +295.0-| +--------1000-| | | | | +------Q6PWR5|Q6P | | | +998.0-| | | | | | +------P06875|PAC | | | | | +-1000-| | +501.0-| +862.0-| +-1000-| +------P07941|PAC | | | | | | | | | +-------------Q7WZI9|Q7W | | | | | +993.0-| | +---------------------------A8GGK2|A8G | | | | | | | +-----------------------------------------A1BBI0|A1B | +-1000-| | | | | +------------------------------------------------A3M5T4|A3M | | | | +869.0-| | +------Q45TR7|Q45 | | | +-------------------------------------------1000-| | | | +------Q60136|PAC | | | | +-------443.0-| +--------------------------------------------------------------Q8CVF4| Q8C | | | | | | +------A1SES8|A1S | | | +-1000-| | | +-------------------------------------------------978.0-| +------A3TPS0|A3T | | | +------| | +-------------Q8YQA9|Q8Y | | | | | | +-----------------------------------------A8LKU3|A8L | | | | | | | | +--------------------Q5LRP7|Q5L | | | | | | | | +504.0-| +624.0-| +------A3SPW1|A3S | | | | | | | +936.0-| | | | | | | +644.0-| +------A6FNR3|A6F | | | | | +848.0-| | | | +867.0-| | | | | +-------------A3SAM5|A3S | | | | +788.0-| +688.0-| | | | | | | | | +---------------------------Q165Q9|Q16 | | | | | | | | | | | +-1000-| | +----------------------------------A3PJP2|A3P | | | | | | | | | | | | | +------------------------------------------------A3JTN7|A3J | | | | | | | | | | +481.0-| +-------------------------------------------------------Q28PW8|Q28 | | | | | | | | | | | | +------Q470H7|Q47 | | | | | | +610.0-| | | | | +209.0-| +-------------------------------------------1000-| +------Q0KAF2| Q0K | | +-1000-| | | | | | | | | | | | +-------------Q1LN15|Q1L | | | | | | | | | | | +429.0-| +---------------------------------------------------------------------Q1AUI0|Q1A | | | | | | | | | | +------Q67TD9|Q67 | | | | | +996.0-| | | | | | | +------Q8CX57|Q8C | | | | +--------------------------------------------------------259.0-| | | | | | +------A7NJ94|A7N | +476.0-| | +974.0-| | | | +------A9B492|A9B | | | | | | +------A0H1F4|A0H | | +------------------------------------------------------------------------------1000-| | | +------A5USU8|A5U | | | | +------B1LYT1|B1L | | +-------997.0-| | | | +------Q2CJE9|Q2C | | | | +----------------------------------------------------------------------922.0-| +------Q0JY93|Q0J | | +-1000-| | | | +------Q1LBI2|Q1L | +995.0-| | | +------A1WN00|A1W | +-1000-| | +------A7CBF7|A7C | +---------------------------------------------------------------------------------------------------------------A2RZ58|A2R From mkkuhner from kingman.gs.washington.edu Tue Jun 10 14:00:10 2008 From: mkkuhner from kingman.gs.washington.edu (Mary K. Kuhner) Date: Tue Jun 10 14:22:57 2008 Subject: [Molecular-evolution] Re: Bootstrap interpretation References: Message-ID: In article , DimitryASuplatov wrote: >I want to generate "random" alignment to use it as a neutral evolution >model for hypothesis testing. I need a phylogenetic tree of my species >for that. >I have used phylip package to generate a set of 1000 replicates, then I >have used PMB model to calculate the distances with protdist and finally >appllied neighbor and consese with default settings. >As a result a have an unrooted tree with bootstrap values generaly >better at the tips than in the center of the tree. In my understanding >this is a normal case, though some values are equal to 25%. >So my question is what could I do with this tree? As I understand, 25% >values emphasize the fact that different parts of distant sequnces do >not show consistency with overall comparison. I can not crop the >alignment. Should I use neighbor-joining to calculate the tree directly >from the alignment? >Thanks. I am having trouble understanding what you want to do here. Let me try to restate it. If I understand correctly, you would like to simulate random data on the same tree that generated your species. You are trying to get this by first making a bootstrap consensus tree of your species, and then (you don't describe this part) simulating data on that tree. This won't work, because the bootstrap consensus tree has no branch lengths, and you need branch lengths to simulate data. The usual approach is simply to infer the tree from your original data (by whatever method you prefer) and simulate data on that inferred tree. While the inferred tree will not be perfect, it should be generally similar to the unknown true tree and may be good enough for a neutrality test. If this is not what you are trying to do, could you restate it? Mary Kuhner mkkuhner@u.washington.edu From mpquast from yahoo.com.br Tue Jun 24 11:48:40 2008 From: mpquast from yahoo.com.br (Monica P. Quast) Date: Wed Jun 25 12:39:28 2008 Subject: [Molecular-evolution] primer design tool Message-ID: <129907.22303.qm@web31305.mail.mud.yahoo.com> Hi everybody! ? Does anyone know (and recomend, of course) a free software or a web tool for primer design? ? Thanks ? Monica ___________________________________ M?nica Paiva Quast Doutoranda/PhD Student Laborat?rio de Macrobentos Marinho Departamento de Zoologia, IB/UNICAMP - Brazil +55 19 3521 6347 __________________________________________________________ Gesendet von Yahoo! Mail. Dem pfiffigeren Posteingang. http://de.overview.mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/mol-evol/attachments/20080624/1654078d/attachment.html