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How to confirm GARD result? (Read 23754 times)

Sundy

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How to confirm GARD result?
Dec 1^st, 2008 at 7:17pm

Hi!
I am using GARD to check recombination for my data. After running GARD on Datamonkey, two breakpoints were found.
My question is: How to verify they are real recombination or not?

The three inferred segment topologies are really different, but I can not figure out which sequence was recombinated from which. So I don't know whether these breakpoints are real recombination sites.

I checked some references, some said Shimodaira and Hasegawa test was used. but they did not say how to perform this test.
Could anyone tell me how to perform SH test? Is there any program to run this test?

I don't have too much knowledge about statistics. It is difficult for me to understand the orginial paper about SH test (Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114–1116.)

Thanks!

Sundy

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to confirm GARD result? Reply #1 - Dec 2^nd, 2008 at 7:39am Dear Sundy, HYPHY includes a GARDProcessor.bf module (see e.g. Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to Login). It takes GARD output files and performs a number of tests on the partitions, including pairwise KH (= SH in this setting) tests. Cheers, Sergei
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Sundy YaBB Newbies Offline Feed your monkey! Posts: 33	Re: How to confirm GARD result? Reply #2 - Dec 2^nd, 2008 at 9:05am Dear Sergei, Thank you very much for your so quick reply.
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Sundy

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Re: How to confirm GARD result?
Reply #3 - Dec 2^nd, 2008 at 11:41am

Dear Sergei,

Sorry to trouble you again.
I am trying to use the HyPhy
Standard Analyses>Recombination>GARDProcessor.bf>
"Please load a nucleotide data file"

After I loaded my sequences data. It required me
"please load a GA partition analysis result file"

My question is "How can I get the GA partition analysis result file"?

Sorry, I am a new learner of HyPhy.
Thanks.

Sundy

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to confirm GARD result? Reply #4 - Dec 2^nd, 2008 at 1:12pm Dear Sundy, It's a file produced by GARD. If you run the online version, it is the one accessible via the [Raw] link, otherwise it is one of the files (ending in splits) output by GARD.bf Cheers, Sergei
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Sundy

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Re: How to confirm GARD result?
Reply #5 - Dec 2^nd, 2008 at 8:22pm

Dear Sergei,

Thank you so much for your quick reply.
I think I finally get some idea about HyPhy ^-^. Really appreciate you!

But I need your help again.
Because I am not sure how to read the results.
I got the following results, after running HyPhy using the GA partition gotten from [Raw] link.

++++++++++++++++
HYPHY 1.0020080508beta(MP) for Windows (Win32) console saved on Tue Dec 2 23:05:11 2008

Loaded 22 model templates from E:\Software\HYPHY_Win32(1)\HYPHY_Win32\SubstitutionModels
Loaded 12 genetic code tables from E:\Software\HYPHY_Win32(1)\HYPHY_Win32\GeneticCodes

2 Intel x86 architecture processors detected.
You can change the number of processors utilized by HyPhy via the HyPhy settings dialog.

Please cite S.L. Kosakovsky Pond, S. D. W. Frost and S.V. Muse. (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679 if you use HyPhy in a publication
If you are a new HyPhy user, the tutorial located at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login may be a good starting point.

Loaded 2 partitions

Sequences :8
Sites :6462
Variable :818

f(A) = 0.289326
f(C) = 0.194309
f(G) = 0.206747
f(T) = 0.309618

c-AIC = 25997
Log Likelihood = -12977.4383434101;
Shared Parameters:
GT=0.160283=0.160283
CT=2.43=2.43
CG=0.0611013=0.0611013
AT=0.402894=0.402894
AC=0.158056=0.158056
alpha=0.010005=0.010005
betaQ=1.59101=1.59101
betaP=0.681693=0.681693

Tree givenTree=((((124_Bat_SARS_273:0.0502577,125_Bat_SARS_279:0.0502527)Node3:0.0610
553,130_PC03_SZ3:0.000585082)Node2:0.000196157,3_HP03E_GZ02:0.000312407)Node1:0,
(15_HP03M_BJ02:0.000620001,31_HP03L_Tor2:0.000150991)Node8:0.000150991,(106_HP04
_GZ0402:0.000620001,PC04_PC4_136_AY613949:0.000312407)Node11:0.00108391);

Mean divergence : 5.25787%

Fitting a single-tree, multiple partition model
Log Likelihood = -10325.9738761955;
Shared Parameters:
S_1=1.40178
betaP=0.681693=0.681693
betaQ=1.59101=1.59101
alpha=0.010005=0.010005
AC=0.158056=0.158056
AT=0.402894=0.402894
CG=0.0611013=0.0611013
CT=2.43=2.43
GT=0.160283=0.160283

Tree tree_0=((((124_Bat_SARS_273:0.0448527,125_Bat_SARS_279:0.0353642)Node3:0.0525925
,130_PC03_SZ3:0.000655097)Node2:0.00020522,3_HP03E_GZ02:0.000171432)Node1:0,(15_
HP03M_BJ02:0.000343505,31_HP03L_Tor2:0.000171517)Node8:0,(106_HP04_GZ0402:0.0005
16532,PC04_PC4_136_AY613949:0.000343924)Node11:0.000688349);
Tree tree_1=((((124_Bat_SARS_273:0.0628736,125_Bat_SARS_279:0.0495728)Node3:0.073723,
130_PC03_SZ3:0.000918301)Node2:0.000287673,3_HP03E_GZ02:0.00024031)Node1:0,(15_H
P03M_BJ02:0.000481519,31_HP03L_Tor2:0.000240429)Node8:0,(106_HP04_GZ0402:0.00072
4064,PC04_PC4_136_AY613949:0.000482105)Node11:0.000964913);

Fitting a mutilple tree, multiple partition model
Log Likelihood = -10315.2583699075;
Shared Parameters:
betaP=0.681693=0.681693
betaQ=1.59101=1.59101
alpha=0.010005=0.010005
AC=0.158056=0.158056
AT=0.402894=0.402894
CG=0.0611013=0.0611013
CT=2.43=2.43
GT=0.160283=0.160283

Tree tree_0=(((((124_Bat_SARS_273:0.0502045,125_Bat_SARS_279:0.0345148)Node4:0.048335
7,130_PC03_SZ3:0.000949729)Node3:9.48274e-05,(106_HP04_GZ0402:0.000783531,PC04_P
C4_136_AY613949:0)Node8:0.000782496)Node2:0,3_HP03E_GZ02:0)Node1:0,15_HP03M_BJ02
:0.000260537,31_HP03L_Tor2:0);
Tree tree_1=((((124_Bat_SARS_273:0.0457419,125_Bat_SARS_279:0.0533774)Node3:0.0870497
,130_PC03_SZ3:0)Node2:0.000706954,31_HP03L_Tor2:0.000707831)Node1:0,(3_HP03E_GZ0
2:0.000706903,15_HP03M_BJ02:0.000707295)Node8:0,(106_HP04_GZ0402:0,PC04_PC4_136_
AY613949:0.00142015)Node11:0.000707243);

Versus the single partition model: c-AIC = 20698.9
Delta AIC = 5298.13

Versus the single tree/multiple partition model: Delta AIC = -2.78213

Partition 1 : 3837 sites
Partition 2 : 1422 sites

Fitting tree 1 to partition 1
Log Likelihood = -7368.17401533097;
Shared Parameters:
betaP=0.681693=0.681693
betaQ=1.59101=1.59101
alpha=0.010005=0.010005
AC=0.158056=0.158056
AT=0.402894=0.402894
CG=0.0611013=0.0611013
CT=2.43=2.43
GT=0.160283=0.160283

Tree aTree=(((((124_Bat_SARS_273:0.0502044,125_Bat_SARS_279:0.0345152)Node4:0.0483353
,130_PC03_SZ3:0.00094992)Node3:9.48549e-05,(106_HP04_GZ0402:0.000783767,PC04_PC4
_136_AY613949:0)Node8:0.000782828)Node2:0,3_HP03E_GZ02:0)Node1:0,15_HP03M_BJ02:0
.000260704,31_HP03L_Tor2:0);

Fitting tree 2 to partition 1
Log Likelihood = -7368.1740159421;
Shared Parameters:
betaP=0.681693=0.681693
betaQ=1.59101=1.59101
alpha=0.010005=0.010005
AC=0.158056=0.158056
AT=0.402894=0.402894
CG=0.0611013=0.0611013
CT=2.43=2.43
GT=0.160283=0.160283

Tree aTree=((((124_Bat_SARS_273:0.0502049,125_Bat_SARS_279:0.034515)Node3:0.0483355,1
30_PC03_SZ3:0.000949661)Node2:9.47293e-05,31_HP03L_Tor2:0)Node1:0,(3_HP03E_GZ02:
0,15_HP03M_BJ02:0.000260946)Node8:0,(106_HP04_GZ0402:0.000783819,PC04_PC4_136_AY
613949:0)Node11:0.000782895);

KH Testing partition 1
Tree 2 base LRT = 1.22224e-06. p-value = 0.4817

Fitting tree 1 to partition 2
Log Likelihood = -2947.08435430648;
Shared Parameters:
betaP=0.681693=0.681693
betaQ=1.59101=1.59101
alpha=0.010005=0.010005
AC=0.158056=0.158056
AT=0.402894=0.402894
CG=0.0611013=0.0611013
CT=2.43=2.43
GT=0.160283=0.160283

Tree aTree=(((((124_Bat_SARS_273:0.0457418,125_Bat_SARS_279:0.0533773)Node4:0.0870492
,130_PC03_SZ3:0)Node3:0.000707349,(106_HP04_GZ0402:0,PC04_PC4_136_AY613949:0.001
41987)Node8:0.000707103)Node2:0,3_HP03E_GZ02:0.000706771)Node1:0,15_HP03M_BJ02:0
.000707307,31_HP03L_Tor2:0.000707425);

Fitting tree 2 to partition 2
Log Likelihood = -2947.08435419031;
Shared Parameters:
betaP=0.681693=0.681693
betaQ=1.59101=1.59101
alpha=0.010005=0.010005
AC=0.158056=0.158056
AT=0.402894=0.402894
CG=0.0611013=0.0611013
CT=2.43=2.43
GT=0.160283=0.160283

Tree aTree=((((124_Bat_SARS_273:0.0457417,125_Bat_SARS_279:0.0533769)Node3:0.0870492,
130_PC03_SZ3:0)Node2:0.000706985,31_HP03L_Tor2:0.000707755)Node1:0,(3_HP03E_GZ02
:0.00070661,15_HP03M_BJ02:0.00070704)Node8:0,(106_HP04_GZ0402:0,PC04_PC4_136_AY6
13949:0.00141997)Node11:0.000707026);

KH Testing partition 2
Tree 1 base LRT = 2.32327e-07. p-value = 0.4839
A total of 0/1 significant couplings
Mean splits identify: 1

+++++++++++++++++

Do we just see these parts?

-------------------
KH Testing partition 1
Tree 2 base LRT = 1.22224e-06. p-value = 0.4817

KH Testing partition 2
Tree 1 base LRT = 2.32327e-07. p-value = 0.4839
A total of 0/1 significant couplings
Mean splits identify: 1
----------------------

Does these mean that the KH test indicates there is no significant evidence (P>0.05) of recombination? The breakpoints are not real recombination sites?

Thank you very much!!
Best regards

Sundy

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Sergei

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Re: How to confirm GARD result?
Reply #6 - Dec 2^nd, 2008 at 10:21pm

Dear Sundy,

You are looking at the correct output for KH tests.

The trees actually appear to be identical (up to some really short internal branches). If GARD returned a significant result, this is due to different branch lengths between partitions, not different topologies. This could be due to ancient recombination events, or due to spatial rate variation.

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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Sundy

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Re: How to confirm GARD result?
Reply #7 - Dec 4^th, 2008 at 1:28pm

Dear Sergei,

Thank you very much for your reply and interpretation.
I analyzed another data set of mine. The datamonkey analysis indicated there are 16 breakpoints. Then I run HyPhy using the spilts file. And I got the results as attached file.

Last part as following:
+++++++++
KH Testing partition 15
Tree 14 base LRT = 0.875094. p-value = 0.0001
A total of 14/14 significant couplings
Mean splits identify: 0.0571429
+++++++++++++++++++++++++++++++

I found that all the p-value = 0.0001 (KH test for 15 partition)

Does this mean that all the breakpoints may be real recombination sites? If it is right, there are too many recombination events.

Or do I need check some other parameters to verify which breakpoints are really significant?

Thank you very mcuh!
Best regards,

Sundy

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to confirm GARD result? Reply #8 - Dec 7^th, 2008 at 6:06pm Dear Sundy, Based on the information you provide, all breakpoints are indeed significant (in the KH sense at least). Not sure what else you can do easily - why do you think there are too many breakpoints? Cheers, Sergei
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Sundy

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Re: How to confirm GARD result?
Reply #9 - Dec 10^th, 2008 at 11:13am

Dear Sergei,

Thank you very much for your replay.
I am just thinking 16 breakpoints means there are 16 times of recombination. It is strange.

I have another question:
If GARD identified only one breakpoint, could KH test verify the significant by using HYPHY?

I have a dataset as attached file, I run GARD and GARDProcessor.bf, and got the results as attached file "30 SARS-Spike HYPHY.txt"

The last part is as following:
KH Testing partition 1
A total of 0/0 significant couplings
Mean splits identify: -nan

I am confused with the "0/0 significant couplings" Is it significant or not? thanks,
and was the meaning of "Mean splits identify: -nan" I know sometime it is a number such as Mean splits identify: 0.116667"

Best regards,

Sundy

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to confirm GARD result? Reply #10 - Dec 10^th, 2008 at 11:15am Dear Sundy, I think that GARDProcessor.bf may be mishandling the case of one breakpoint at reporting stage. Can you send me your files so that I can confirm and fix the issue? Cheers, Sergei
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Sundy YaBB Newbies Offline Feed your monkey! Posts: 33	Re: How to confirm GARD result? Reply #11 - Dec 10^th, 2008 at 11:15am I forgot the attachment
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Sundy YaBB Newbies Offline Feed your monkey! Posts: 33	Re: How to confirm GARD result? Reply #12 - Dec 10^th, 2008 at 11:25am Dear Sergei, Thank you very much. Actually, I have three datasets as the attached file. I am trying to detect the recombination for them. Could you pleas help me to check? I would greatly appreciate! Best regards, Sundy
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Sundy YaBB Newbies Offline Feed your monkey! Posts: 33	Re: How to confirm GARD result? Reply #13 - Dec 10^th, 2008 at 11:34am Because the sequences of Bat-SARS are quite difference with the other sequences, I tried to performed GARD for 4 BAT-SARS sequences and other sequences separately. I got lots of breakpoints for 4 BAT-SARS sequences in each dataset, and only 1 or 0 breakpoint for the other sequences. Thank you very much! Sundy
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Sergei

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Re: How to confirm GARD result?
Reply #14 - Dec 11^th, 2008 at 8:19am

Dear Sundy,

The reason you were getting 'nan' with GARDProcessor.bf was because it expects the _splits file to start with two blank likes (for no other reason as to be compatible with an old formatting quirk in GARD) and if they are not there - it will not read the data correctly. E.g. here is the _splits file for your G4-SARS-59S file.

Quote:

0-1490
(((((((((((((PC03_SZ13_AY304487_0305:0,PC03_SZ1_AY304489_0305:0):0.000638888,PC0
3_SZ3_AY304486_0305:0.000639661):0.00201
583,((Bat_SARS_273_DQ648856_S:0.285893,((Bat_SARS_279_DQ648857_S:0.123077,Bat_SA
RS_Rp3_DQ071615_S:0.0872019):0.030949,Ba
t_SARS_HKU3_DQ022305_S:0.0962264):0):1.6738,((((HP03E_GZ02_AY390556:0,HP03L_GD01
_AY278489:0):0.00123832,((HP03E_HGZ8L1_A
_AY394981_CG:0,HP03E_ZS_A_AY394997:0):0.000614304,HP03M_JMD_AY394988_CG:0):0.000
614595):0,HP03M_BJ02_AY278487:0.00123514
):0.000623404,(((((HP03E_HGZ8L1_B_AY394982_CG:0,(((HP03M_BJ04_AY279354:0.0006134
59,HP03M_HZS2_Fb_AY394987:0):0,((((((((H
P03L_Tor2_NC_004718:0,(HP03L_Sin3765V_AY559084:0,HP03L_Sin845_AY559093:0.0006127
55):0.000612974):0,HP03L_AS_AY427439:0):
0,HP03L_Frank_AY291315:0):0,HP03L_GZ_B_AY394978:0):0,HP03L_SH_QXC1_AY463059:0):0
,HP03L_GZ_C_AY394979:0.00061234):0,HP03L
_CUHK_LC2_AY394999:0.00061388):0,HP03L_Sino1_11_AY485277:0.000613116):0.00061234
):0.00061234,(HP03M_GZ50_AY304495:0,HP03
M_GZ_A_AY394977_CG:0.00061234):0.000612479):0):0,HP03E_HSZ_Bb_AY394985:0):0,HP03
E_HSZ_Cb_AY394986:0):0,HP03M_HZS2_C_AY39
4992:0):0,HP03M_BJ03_AY278490:0.000613006):0.00124613):0.00198581):0):0.00329353
,(((PC04_A021_AY687356_S:0,PC04_HC_SZ_DM
1_AY545915:0):0.000644733,PC04_B024_AY687360_S:0):0.00128397,(((PC04_A022_AY6868
63:0,PC04_B029_AY687361_S:0):0,PC04_cive
t007_AY572034:0):0.000630181,(PC04_C025_AY687370_S:0,PC04_HC_SZ_61_AY515512:0.00
0627921):0):0):0.00130383):0,(PC04_A001_
AY687354_S:0,PC04_C013_AY687365_S:0.00061531):0):0.000616592,(PC04_PC4_13_AY6139
48:0.000636761,PC04_HC_SZ_79_AY545914:0.
000618928):0.000618842):0,(PC04_C029_AY687372_S:0.000596247,CFB04_SZ_AY545919:0.
00126154):0.000636761):0,((((PC04_PC4_11
5_AY627044_S:0,(HP04_GZ0401_AY568539:0.0012382,HP04_GZ0402_AY613947:0.000612695)
:0):0,PC04_PC4_241_AY627048_S:0):0,PC04_
B012_AY687359_S:0):0.000623871,PC04_PC4_137_AY627045_S:0):0.00061709):0,PC04_C01
8_AY687368_S:0.00061521):0,PC04_PC4_136_
AY613949:0):0,PC04_PC4_199_AY627047:0):0,PC04_A013_AY687355_S:0):0,(PC04_PC4_205
_AY613952_S:0.000615257,PC04_C028_AY6873
71_S:0):0,PC04_B033_AY687362_S:0.000614959)
1491-3764
(((((((((((((((((PC03_SZ13_AY304487_0305:0,PC03_SZ1_AY304489_0305:0.0019):0.0009
70853,PC03_SZ3_AY304486_0305:0):0.001926
45,(Bat_SARS_273_DQ648856_S:0.171533,((Bat_SARS_279_DQ648857_S:0.0436005,Bat_SAR
S_Rp3_DQ071615_S:0.0409013):0.0288179,Ba
t_SARS_HKU3_DQ022305_S:0.133101):0.0316166):0.126907):0.000946349,((((HP03E_HGZ8
L1_A_AY394981_CG:0.000471595,HP03L_GD01_
AY278489:0.000948031):0,HP03E_ZS_A_AY394997:0):0.000474592,(((((((((HP03E_HGZ8L1
_B_AY394982_CG:0,(((HP03M_BJ03_AY278490:
0.000959516,((HP03M_BJ04_AY279354:0.000477548,((HP03M_HZS2_C_AY394992:0,HP03L_Fr
ank_AY291315:0):0.000477139,(HP03L_Tor2_
NC_004718:0,HP03L_SH_QXC1_AY463059:0.00144432):0.000476845):0):0,HP03L_GZ_B_AY39
4978:0.00047722):0):0,HP03L_GZ_C_AY39497
9:0.000959516):0,HP03L_CUHK_LC2_AY394999:0.000477047):0):0,HP03M_BJ02_AY278487:0
):0,HP03M_HZS2_Fb_AY394987:0):0,HP03L_AS
_AY427439:0):0,HP03L_Sino1_11_AY485277:0):0,(HP03L_Sin3765V_AY559084:0.000481251
,HP03L_Sin845_AY559093:0.000482511):0.00
0958175):0.000477356,HP03M_GZ50_AY304495:0):0,HP03M_GZ_A_AY394977_CG:0):0,HP03M_
JMD_AY394988_CG:0):0):0.000477349,(HP03E
_HSZ_Bb_AY394985:0,HP03E_HSZ_Cb_AY394986:0.000477285):0):0.00047524):0,HP03E_GZ0
2_AY390556:0):0.0014118,HP04_GZ0402_AY61
3947:0.00194111):0.000990094,PC04_PC4_137_AY627045_S:0.000481253):0.000472576,PC
04_PC4_199_AY627047:0):0.000465501,(PC04
_PC4_241_AY627048_S:0.000472816,PC04_B012_AY687359_S:0.000943099):0.000475402):0
,(PC04_B024_AY687360_S:0.000465766,PC04_
C018_AY687368_S:0):0.000465963):0,(PC04_A021_AY687356_S:0.000481484,(((PC04_A022
_AY686863:0.000465646,PC04_civet007_AY57
2034:0):0,PC04_HC_SZ_61_AY515512:0):0,PC04_HC_SZ_79_AY545914:0):0):0.000465906):
0,PC04_PC4_136_AY613949:0.000465727):0,P
C04_PC4_13_AY613948:0):0,PC04_B029_AY687361_S:0):0,PC04_HC_SZ_DM1_AY545915:0):0,
((HP04_GZ0401_AY568539:0,PC04_A013_AY687
355_S:0.000465665):0,PC04_C029_AY687372_S:0):0):0,((((PC04_PC4_115_AY627044_S:0,
PC04_C028_AY687371_S:0.000935622):0,PC04
_PC4_205_AY613952_S:0):0,PC04_B033_AY687362_S:0):0,CFB04_SZ_AY545919:0):0,((PC04
_A001_AY687354_S:0,PC04_C025_AY687370_S:
0.000465657):0,PC04_C013_AY687365_S:0):0)

It is actually quite common to lose power in breakpoint detection as you increase the number of sequences. Think of it as signal dilution: 1/4 recombinant sequences in a 4-taxon analysis is more obvious than 1/50 recombinant sequences in a 50-taxon analysis (of course it depends on the sequences involved, and how strong the recombination signal is). Also, while it is possible to infer a 4-taxon tree from a short sequence (e.g. 100bp) somewhat accurately, doing so for a 50-taxon tree is less likely - hence you lose breakpoints in the noise.

Cheers,
Sergei
HTH,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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