Hi, can you write about this function and what is the best way to use it? as I have data set of different lentiviruses integrase sequenses and i try to make sense from it.

I got different results which seems not to make sense

I am newbie so any help here is wellcome...

Thanks

Hi Sergei, So here what i did I hope that you can correct my mistakes

in the first step I selected the best model for tree using tree model and build max likelihood tree (GTR+G+I). Once the tree
was done I used the swap alogrithem of hyphy to find better tree. Then I took this tree and tried to see if the null hypothesis of strict Molecular clock validity which in my case was regected as expected when i used a single rate model (F84) for the clock tree but was not regected when I used the GTR+G+I model. On the other hand when I used the tipdate function and I put for the clock the same model that I used for the tree, the tree was regected (P=0) again.

Now my question is how I can estimate the true evolution rate/site/year when the tree is regected?

If you can highlight me on the correct procedure for this function it will be great.

Thanks
Great software 

Thanks for the fast response,can you elaborate on how to add the synonomus rates with the tipdate.bf ?

Thanks Sergei on your fast response you are great
I want to ask if I may about the new Bf file that can deal with situations in which the clock model fail, I think it will will be graet addition to this program that from what I see is far better than many others...

So when its going to be added?

Hi Sergei, any new news on the procedure (Bf file) for estimating rates when a simple clock fails?

Best wishes
Promi

Hi Sergei, sorry to bother you but is the new dating bf file avilable?

Have nice day
Promi

Hi, 
I tried to use this .bf, but I've one message of error after that I chose the units of my system.
The dataset and the tree have the year date of collected, like the example on the Tipdate.

Best,

Jackson


---- RUNNING MOLECULAR CLOCK ANALYSIS WITH DATED TIPS----
The underlying methodology developed by Andrew Rambaut is discussed
in Bioinformatics 16(4): 395-399
The following data was read:
201 species:{1Sim1958,2Hum2000,3hum2000,4Hum1999,5Hum2003,6Hum2001,7Hum2000,8Hum1997
,9Bov2005,11Hum2004,12Hum2004,13Hum1995,14Hum2002,15Hum2000,16Hum2001,17Hum1997,
19Hum2004,20Hum2004,21Hum1997,24Hum1997,42Hum1997,43Hum1997,50Sim1990,51Por2004,
53Por2004,55Fel1993,56Fel1993,57Fel1993,58Fel1993,61Fel1989,62Hum1982,8247228Hum
,63Hum1997,64Hum1996,65Hum1996,67Hum1995,68Hum1995,69Hum1996,70Hum1992,71Hum1992
,72Hum1992,73Hum1991,74Hum1991,75Hum1990,77Hum1993,78Hum1990,79Hum1990,82Hum1996
,84Hum1996,85Hum1997,87Hum1996,89Hum1997,91Hum1996,95Hum1996,98Hum1996,100Hum199
6,101Hum1996,105hum1996,106Por1980,107Hum2002,108Hum1998,109Hum1997,110Hum1998,1
11Hum1993,112Hum1999,113Hum2000,114Hum1990,115Hum1998,116Hum2000,117Bov2001,118L
am1981,119Rab2001,120Rab2001,121Rab2001,122Rab1996,123Cap1998,124Hum1995,125Hum1
995,126Hum1992,127Hum1990,128Hum1991,129Hum1991,130Hum1980,131Hum1981,132Hum1983
,133Hum1982,134Hum1990,135Hum1981,136Hum1977,137Hum1980,138Hum1989,139Hum1990,14
0Hum1992,141Hum1986,142Hum1992,144Lap1978,145Hum1993,151Hum1996,152Hum1997,153Hu
m1997,154Hum1997,155Hum1997,156Hum1997,159Hum1997,160Hum1997,161Hum1997,162Hum19
97,164Hum1998,166Hum1998,167Hum1998,168Hum1996,169Hum1998,170Hum1998,171Hum1998,
172Bov1981,173Bov1973,174Bov1973,175Hum1986,176Hum1980,177Hum1984,178Hum1990,179
Hum1990,180Hum1990,181Hum1990,182Hum1988,183Hum1988,184Hum1988,185Hum1988,186Hum
1976,187Hum1994,189Hum1993,190Hum1992,191Hum1983,192Hum1982,193Hum1981,194Hum198
5,195Hum1985,196Hum1985,201Hum1989,202Hum1995,203Hum1993,204Hum1992,205Hum1981,2
06Hum1978,207Hum1994,208Hum1994,209Hum1993,210Hum1994,211Hum1994,212Hum1995,220H
um1995,231Hum1998,232Hum1996,233Hum1974,234Hum1996,235Hum1994,236Hum1997,237Hum1
997,238Por1987,239Can1980,240Equ1981,241Equ1981,242Equ1976,243Equ1975,244Por1987
,245Por1987,246Por1987,247Lap1988,248Lap1988,249Lap1978,250Lap1983,251Rot1984,25
2Por1976,253Hum1981,254Hum1975,255Hum1982,256Hum1993,257Hum1993,258Hum1981,260Hu
m1990,261Hum1988,262Hum1987,263Hum1986,264Hum2004,267Hum2004,268Hum2004,271Hum20
03,272Hum2003,274Hum2003,275Hum2003,276Hum2003,277Hum2003,278Hum2002,279Hum2002,
282Hum2002,283Hum2002,286Hum2002,287Hum2001,289Hum2001,290Lap2004,291Mur1982};
Total Sites:761;
Distinct Sites:469
What units are the dates measured in (e.g. months)? This is only used for reporting the results.years

ERROR: Input tree must contain date information in the chosen format for all sequences.
Branch lengths for internal nodes are ignored.

Dear Jackson,

One of the sequences names must not be recognized.
If you download today's version of HyPhy, DatedTipsMolecularClock.bf will report which sequence failed to match the expected format - you should be able to debug it from there.

Cheers,
Sergei