partitioned matrix: dna + morphology

[max maronna]

Hi Derrick and Garli users,

I´m trying to run a partitioned analysis, considering several partitions (dna data) combined with a morphological matrix.

I read the garli´s wiki
https://www.nescent.org/wg_garli/Using_partitioned_models#Dividing_up_the_data

and I define my taxa block and dataset (3 molecular markers and a morphological dataset with 32 characters) as 7 different characters blocks.

Defining the characters sets and partitions (partitions for dna were defined in partition finder), I tried

begin sets;
    charset 16s = 1-404;
    charset coi_1 = 405-1037\3;
    charset coi_2 = 406-1037\3;
    charset coi_3 = 407-1037\3;
    charset coii_1 = 1038-1403\3;
    charset coii_2 = 1039-1403\3;
    charset coii_3 = 1040-1403\3;
    charset morfo = 1004-1435;

charpartition pfinder = chunk1:16s, chunk2:coi_1, chunk3:coi_2, chunk4:coi_3 coii_3, chunk5:coii_1, chunk6:coii_2, chunk7:morfo;
END;

It didn´t work: Garli log file said:

----------------------------------
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
    16s_coi_coii_pfinder_morfo.nex ...
Reading TAXA block... successful
Reading CHARACTERS block... found dna data... successful
Reading CHARACTERS block... found dna data... successful
Reading CHARACTERS block... found dna data... successful
Reading CHARACTERS block... found standard data... successful
Reading SETS block...
Error in the Character descriptor of a CharSet command.
Expecting a character name or a number corresponding to a character's number (a number from 1 to 32). Found 404
Line:   102
Column: 25

ERROR: NCL encountered a problem reading the dataset.

----------------------------------

Line 102 is "charset 16s = 1-404;" in the original nexus file...

I don´t know what I´m doing wrong...any idea?

Thanks in advance, best

max

[cmtr...@gmail.com]

Has any one taken a look at this? I could use an answer too that's similar. 

[Derrick Zwickl]

Hi All,

I'm sorry, but Garli Documentation and Support has been in a sad state for a while due to issues largely beyond my control.

To clarify the state of things a bit:
-The documentation wiki now lives at github: https://github.com/zwickl/garli/wiki
-The most recent source code and examples are also at githu: https://github.com/zwickl/garli
-For the moment executables are still best obtained from googlecode (https://code.google.com/archive/p/garli/downloads) but I hope to add them to github soon

-------
As for the specific question regarding partitioned analyses with multiple dna subsets plus morphology data, configuration is confusing for this use case and documentation has not been available.

I just added wiki documentation for it.  Let me know if it is comprehensible (for basic comments, using garli....@gmail.com would probably be better that spamming this list):

https://github.com/zwickl/garli/wiki/Partitioned_DNA_and_morphology

Thank you to those valiant people who tried to figure this out on their own.  It would always have been possible to extract the desired sites for each partition subset into different characters blocks yourself (i.e., one characters block containing only first positions, etc), but that would be a pain and shouldn't be necessary.  In the documentation linked above you'll see that the other way of doing it isn't much more pleasant.

Again, sorry for the confusion.

Best,
Derrick

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