Re: [dartR] Phylogenetic tree from the DArTseq SNP data
Peter Unmack
distances.
gl2fasta(gl, method=3, outfile="filename.fas", outpath=getwd())
If you create a field in your metadata file called phylo_label you can
define the labels for each sequence and have them included by running
these commands prior to using the gl2fasta command above.
pop(gl)<- rep("",nInd(gl))
indNames(gl)<- gl@other$ind.metrics$phylo_label
Once you have the fasta file you need to import it / convert it so you
can use raxml, or a bayesian program to run a phylogenetic analysis.
Cheers
Peter Unmack
On 29/05/2023 3:07 pm, Divya SHAJI wrote:
> Hi,
>
> I would like to construct a Phylogenetic tree from the DArTseq SNP data.
> I am using the following code. I am not sure whether this code correct
> or not.
>
>> library(dartR)
>
>> gl <- gl.read.dart(filename="/home/user/Desktop/testset.csv")
>
>> saveRDS(gl, file="gl.Rdata")
>
>> gl <- readRDS("gl.Rdata")
>
> For creating a distance matrix
>
> D <- utils.dist.ind.snp (gl, method='Euclidean',scale=TRUE)
>
> capture.output (D, file = "output.tab", append = TRUE)
>
>
> How do I create a phylogenetic tree from the distance matrix?
>
> Thank you so much for your time and consideration.
>
> Best regards,
>
> Divya.
>
>
>
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Divya SHAJI
GNTACTCGTNGTCNTGTCAGCATTAGGTGGAGATTGTCCCTNATATTCGTGCGCAATTGTTNNAGCGANGCAGAACGGNGTNGGGCCNGCCGTNTAGACNAACCCTNGCCAGTAGNNNTNACGAAAAGGCNGNAGACACGCNCANCGCCCAGACCCTCGCGGAGGCGNCGGCAAATNNNCTTTCTCTTGNAARTTNNAAGGACTAGCAAAAATGCTTGAATATATNCCCGTTCCGGTTTTNCCTTCCTANTGGCA
>_
GNTACTCGTNGTCTTGTCAGCATTAGGTGGAGATTGTCMCTNATATTCGTGCGCAATTGTTNNAGCGANGCAGAACGGNGTNGGGCCNGCCGTNTAGACGAASCCTGGCCAGTAGAGNTNNCGAAAAGGCNGNANACACGCNCANCGCCCAGACCCTCGCGGAGGCGNCGRCAAATNNNCTTTCTCTTGNAAAYNNNAAGGACTAGCAAAAATGCTTGAATATATNCCCGTTCCGGTTTTNCCTTCNTANTGGCA
Arthur Georges
Bernd.Gruber
HI Divya,
I assume you have not named your loci.
This can be tested with
locNames(gl)
if this is returning empty/null then you could do the following
locNames(gl)<- gl@other$loc.metrics$AlleleID
to name them accordingly. Assuming the alleleID is in you metadata.
And then rerun gl2fasta
Cheers, Bernd
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Divya SHAJI
[1] "100049687-12-A/G" "100049698-16-C/T" "100049728-23-T/G"
[4] "100049805-56-A/T" "100049816-51-C/T" "100049839-39-A/T"
[7] "100049926-33-C/T" "100049990-20-G/T" "100050079-57-T/G"
indNames(gl)<- gl@other$ind.metrics$phylo_label
Processing genlight object with SNP data
Warning: Dataset contains monomorphic loci which will be included in the output fasta file
Assigning ambiguity codes to heterozygote SNPs, concatenating SNPs
Removing loci for which SNP position is outside the length of the trimmed sequences
Generating haplotypes ... This may take some time
Completed: gl2fasta
NULL
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Bernd.Gruber
Hi Divya,
My mistake the gl2fasta is by individuals
Can you make sure that there is no typo
gl@other$ind.metrics$phylo_label
should produce the individuals names can you check that.
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Divya SHAJI
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Bernd.Gruber
Then your phylolabel are not set correctly, you need to find one or just
indNames(gl) <- paste0(“Ind_”,1:nInd(gl))
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Divya SHAJI
>
library(dartR)
>
gl <- gl.read.dart(filename="/home/user/Desktop/testset.csv")
>
saveRDS(gl, file="gl.Rdata")
>
gl <- readRDS("gl.Rdata")
>
pop(gl)<- rep("",nInd(gl))
indNames(gl)<-
gl@other$ind.metrics$phylo_label
>
gl2fasta(gl, method=3, outfile="filename.fas",
outpath=getwd())
Thank you for your help.
Regards,
Divya.
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Bernd.Gruber
You need to retype the quotes, if you copy it from the email they become the wrong type of character.
Cheers, Benrd
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Jose Luis Mijangos
The function gl2fasta first concatenates individual names and the population name of each individual, and then this information is used as the name for each FASTA sequence.
First, check that the fields for individual names and population names are there:
> indNames(testset.gl)
> popNames(testset.gl)
If these fields are not there, you will see the word "NULL" in the R console.
One way to input this information into these fields is by using a CSV file when you read your DArT report into dartR using the function gl.read.dart(). Please check our tutorial starting on page 8 regarding how to input this information into dartR:
You can find our other tutorials at:
Alternatively, you could assign dummy names, for example:
> # assigning numbers as individual names
> indNames(testset.gl) <- as.character(1:nInd(testset.gl))
> # assigning "pop1" to all individuals
> pop(testset.gl) <- rep("pop1",nInd(testset.gl))
Then, when using the gl2fasta function, each sequence will be named:
> gl2fasta(testset.gl, method=3, outfile="filename.fas", outpath=getwd())
Cheers,
Luis