Hello!

I'm trying to estimate the sustitution rate of some region of Hepatits C Virus.
I've several (7) samples of a patient spanning several years.
Up to now I've 2 estimations, one with BEAST using cloned sequences of each sample, and a "quick and dirt" estimation by linear regresion of branch length over time in the best tree (I say "the best", because it was the result of an exhaustive search with the best fit model) of direct sequences (7 taxa).
Some time ago I've used DatedTips to estimate this rate which was an order of magnitude less than the other estimations.
I'm trying to perform the GADatedClock analysis.
I've the sequences, the tree, set local or global estimations, and always get an error:

Expression syntax/semantics error.
Current BL Command:ExportAMatrix(modelFile,StringToMatrix(currentPopulation[populationSize-1]),1,1) Current Task has been terminated. Would you like to see the remaining error...

and the program stops.

Here is the output of the console:

What units are the dates measured in (e.g. months. This is only used for reporting the results.)?days
Read the following dates:
Nov1998_16301:      16301      days
Jul1999_16524:      16524      days
Mar2000_16772:      16772      days
Feb2002_17490:      17490      days
Ago2006_19107:      19107      days
Oct2001_17356:      17356      days

______________FREE RATES______________
Log Likelihood = -1146.88982261698;
Shared Parameters:
R=0.494877=0.494877

Tree givenTree=(Nov1998_16301:0.00676707,Jul1999_16524:0,(Mar2000_16772:0.0107896,(Fe
b2002_17490:0.00564523,(Ago2006_19107:0.0309347,Oct2001_17356:0.00512011)50:0.00
606189)28:0.0071273)98:0.0200414);

BEST AIC=2313.78
Fitting the single rate model...
Pass 1(0) log-L = -1155.32
Pass 2(1) log-L = -1155.32
Pass 3(2) log-L = -1155.32

______________SINGLE RATE______________
Log Likelihood = -1155.32412978027;
Shared Parameters:
clockTree_scaler_0=0.373943
R=0.494877=0.494877

Tree clockTree=(Nov1998_16301:0.00617536,Jul1999_16524:0.0102448,(Mar2000_16772:0.004
91676,(Feb2002_17490:0.0101288,(Ago2006_19107:0.0357021,Oct2001_17356:0.00374861
)50:0.00393489)28:0.0078905)98:0.00985373);

AIC=2320.65


Starting GA with 2 rate classes
Baseline Model Fit
c-AIC = 2320.65
Starting the GA now...
Generation 2 with 2 rate classes.
Best c-AIC found far is 2310.53
This is a 10.1221 improvement over the single-rate model
GA has considered 29 unique models so far
Total run time so far is 0 hrs 0 mins 4 seconds
Average cluster time per generation is  4.00 seconds
Average CPU time per model is  0.14 seconds
Convergence criterion: 0/50

Other usefull data...
Model HKY
OS: Windows SP3
HyPhy Version: 1.0020080508

Any suggestions to solve this issue?

Thanks in advance!

Andrés

Thank you very much.
I've used version 2.0 of HyPhy for windows and I've got similar error, however using the version compiled from svn in linux I was able to complete the analysis. (only after tunning my regional configuration switching "," per ".")
I wonder if there is any suggested bibliography in order to understand the theoretical framework behind this analysis.
I'm familiar with phylogenetics analysis with distance, parsimony, maximum likelihood and bayesian methods... also know something about genetic algorithms.

Thank you!

Andrés

Thanks!

BTW, Is there some way to load decimal dates (i.e. 42.32 years) in any of the tip dates analysis? (the load tree script does not like "." in leaf names)

Hi Andres,

I am impressed with your patience digging through HyPhy source code! In HyPhy language '.' is similar to 'member access' in C, i.e. "tree.node.variable". Adding a '.' inside the node name would break a lot of downstream dependancies. The easiest thing to do is simply to convert all the dates to integers (up to a given precision, e.g. by multiplying the dates by 100).

Sorry there isn't an easier fix.

Sergei

Hi Andres,

That will work too; I suggest using the underscore symbol, as it will be accepted by the tree parser.

Sergei