[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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