[Molecular-evolution] Bootstrap interpretation

DimitryASuplatov via mol-evol%40net.bio.net (by genesup from gmail.com)
Mon Jun 9 08:20:48 EST 2008


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



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