Article View: bionet.molbio.evolution
Article #469Bootstrap interpretation
From: DimitryASuplatov
Date: Mon, 09 Jun 2008 13:20
Date: Mon, 09 Jun 2008 13:20
184 lines
9100 bytes
9100 bytes
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
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+------A5V4S1|A5V
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+---------------------364.0-|
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| +------Q8VQG6|Q8V
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| +------Q83YY8|Q83
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+295.0-| +--------1000-|
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| | | +------Q6PWR5|Q6P
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| | +998.0-|
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| | | | +------P06875|PAC
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| | | | +-1000-|
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+501.0-| +862.0-| +-1000-| +------P07941|PAC
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| | +-------------Q7WZI9|Q7W
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| +993.0-|
| +---------------------------A8GGK2|A8G
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+-----------------------------------------A1BBI0|A1B
| +-1000-| |
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+------------------------------------------------A3M5T4|A3M
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| +869.0-| |
+------Q45TR7|Q45
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+-------------------------------------------1000-|
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+------Q60136|PAC
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| +-------443.0-|
+--------------------------------------------------------------Q8CVF4|
Q8C
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+------A1SES8|A1S
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+-1000-|
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+-------------------------------------------------978.0-|
+------A3TPS0|A3T
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+------| |
+-------------Q8YQA9|Q8Y
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+-----------------------------------------A8LKU3|A8L
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| +--------------------Q5LRP7|Q5L
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+504.0-| +624.0-| +------A3SPW1|A3S
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| | | +936.0-|
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| | +644.0-| +------A6FNR3|A6F
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| +848.0-| |
| | +867.0-| |
| | | +-------------A3SAM5|A3S
| | | | +788.0-|
+688.0-| |
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| +---------------------------Q165Q9|Q16
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| | | | +-1000-| |
+----------------------------------A3PJP2|A3P
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+------------------------------------------------A3JTN7|A3J
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| | | | +481.0-|
+-------------------------------------------------------Q28PW8|Q28
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+------Q470H7|Q47
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+610.0-|
| | | | +209.0-|
+-------------------------------------------1000-| +------Q0KAF2|
Q0K
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+-------------Q1LN15|Q1L
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| | | | +429.0-|
+---------------------------------------------------------------------Q1AUI0|Q1A
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+------Q67TD9|Q67
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+996.0-|
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| +------Q8CX57|Q8C
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+--------------------------------------------------------259.0-|
| | | |
| +------A7NJ94|A7N
| +476.0-| |
+974.0-|
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+------A9B492|A9B
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+------A0H1F4|A0H
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+------------------------------------------------------------------------------1000-|
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+------A5USU8|A5U
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+------B1LYT1|B1L
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+-------997.0-|
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| +------Q2CJE9|Q2C
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+----------------------------------------------------------------------922.0-| +------Q0JY93|Q0J
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| +-1000-|
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| | +------Q1LBI2|Q1L
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+995.0-|
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| +------A1WN00|A1W
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+-1000-|
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+------A7CBF7|A7C
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+---------------------------------------------------------------------------------------------------------------A2RZ58|A2R
Technical Details
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