Error in MSA2dist::cds2aa unused argument (return.cds = TRUE)

[karthickbrlab]

HI..

how to solve this

K1 |> MSA2dist::cds2aa(shorten=TRUE, return.cds=TRUE) |> MSA2dist::dnastring2kaks(model = "YN") Error in MSA2dist::cds2aa(K1, shorten = TRUE, return.cds = TRUE) : unused argument (return.cds = TRUE)

MSA2dist::dnastring2kaks(cds1, model = "YN") Error in MSA2dist::dnastring2kaks(cds1, model = "YN") : Error: input needs to be a DNAStringSet

[kullrich]

Hi, it seems that you have not installed the development version, to do so:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MSA2dist")

[karthickbrlab]

Hi..

Installed it, Does the ka/ks ratio be infinite?

I got quite different results in different models. Which one is a go to model for chloroplast genes.

On Tue, Apr 2, 2024 at 12:04 PM Kristian Ullrich @.***> wrote:

Hi, it seems that you have not installed the development version, to do so:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

The following initializes usage of Bioc devel

BiocManager::install(version='devel')

BiocManager::install("MSA2dist")

— Reply to this email directly, view it on GitHub https://github.com/kullrich/kakscalculator2/issues/3#issuecomment-2031181586, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBQ4H4ZUDBYUKVKA5YEVBCTY3JGP7AVCNFSM6AAAAABFSWH4N2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZRGE4DCNJYGY . You are receiving this because you authored the thread.Message ID: @.***>

[kullrich]

Hi, yes, if e.g. there are only non-synonymous changes in a gene and no synonymous change.

You could try to compare the models against e.g. http://www.hyphy.org results or http://abacus.gene.ucl.ac.uk/software/paml.html to select a model that fits your data.

Here you would find a python script to run codeml:

https://github.com/kullrich/bio-scripts/blob/master/fasta/cds2codeml.py

Best regards

[karthickbrlab]

Well.. Then could we say the gene has obvious positive selection?

On Wed, 3 Apr, 2024, 12:10 pm Kristian Ullrich, @.***> wrote:

Hi, yes, if e.g. there are only non-synonymous changes in a gene and no synonymous change.

You could try to compare the models against e.g. http://www.hyphy.org results or http://abacus.gene.ucl.ac.uk/software/paml.html to select a model that fits your data.

Here you would find a python script to run codeml:

https://github.com/kullrich/bio-scripts/blob/master/fasta/cds2codeml.py

Best regards

— Reply to this email directly, view it on GitHub https://github.com/kullrich/kakscalculator2/issues/3#issuecomment-2033674566, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBQ4H475QLQDDBSHCS26TATY3OP5BAVCNFSM6AAAAABFSWH4N2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZTGY3TINJWGY . You are receiving this because you authored the thread.Message ID: @.***>

[kullrich]

If one consider Ka/Ks ratio of > 1 as positive selection yes.

Anyhow, normally one at least should look at a distribution of Ka/Ks values of your query species and compare with this distribution. Since I am not an expert in mito evolution at least you could also look into another published data set and compare to the signatures that have been found in another independant data set.

[kullrich]

Since this issue is not related to kakscalculator2 anymore, I am closing this issue here now.

Best regards

[karthickbrlab]

hi..

So how could I cite MSA2dist??

On Wed, Apr 3, 2024 at 12:56 PM Kristian Ullrich @.***> wrote:

Closed #3 https://github.com/kullrich/kakscalculator2/issues/3 as completed.

— Reply to this email directly, view it on GitHub https://github.com/kullrich/kakscalculator2/issues/3#event-12336353045, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBQ4H467FT2NBCCWYLZ2RSLY3OVLDAVCNFSM6AAAAABFSWH4N2VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJSGMZTMMZVGMYDINI . You are receiving this because you authored the thread.Message ID: @.***>

[kullrich]

Ullrich K (2023). MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. doi:10.18129/B9.bioc.MSA2dist, R package version 1.6.0, https://bioconductor.org/packages/MSA2dist.

[karthickbrlab]

Thanks

On Thu, 18 Apr, 2024, 3:08 pm Kristian Ullrich, @.***> wrote:

Ullrich K (2023). MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. doi:10.18129/B9.bioc.MSA2dist https://doi.org/10.18129/B9.bioc.MSA2dist, R package version 1.6.0, https://bioconductor.org/packages/MSA2dist.

— Reply to this email directly, view it on GitHub https://github.com/kullrich/kakscalculator2/issues/3#issuecomment-2063449583, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBQ4H467AEO6BA7ZXYGTMBTY56IAXAVCNFSM6AAAAABFSWH4N2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRTGQ2DSNJYGM . You are receiving this because you authored the thread.Message ID: @.***>