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Dear Developer,
i am running the ks caculator as follows:
the input file is cds alignment file between two strains of my species i want to compare. this input file i generated with the pal2nal.pl with two strains protein file and cds files.

./kakscalculator2/bin/KaKs_Calculator -i blasia_helsinki_potsdam_cds.aln -o blasia_helsinki_potsdam_genes_ks.txt -m YN

This is the error:
Error. The size of two sequences in 'TRINITY_DN748_c0_g3_i4.p1 GAGGCAGCTGAGATAGTTCGAGCTTGTATGGAGGGAGTGGCGTCACTGAAAGTTCCACTT' is not equal.

this gene id "TRINITY_DN748_c0_g3_i4.p1 " is the first gene id in the alignment file.

Could you help with this?
Thanks a lot!
Cheers,
Yuling

Dear author,

Thanks for making this useful program.

I noticed that KaKsCalculator seems to run for a long time. How can use multiple cpus/threads to make the job faster?

I have 27 thousand pairs to calculate their KaKs values, and so far only 500 pairs were processed in 12 hours. I am using 32 cpus but I am not sure in the KaKsCalculator is using them.

My command is below, so I am using the default MA method:

KaKs_Calculator -i lmlp24chr.cds.aln.axt -o lmlp24chr.cds.aln.axt.kaks

My axt file has the pairs like the below. As mentioned I have 27K of these pairs.

Lm_g1002.t1-Lp_g998.t1
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACT
ATAGCTGCTCGGCTAATTGTCTTAGCAACTATAGCTGCTCGGCTAATTGTCTTAGCAACT
ATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTAT
CTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT
ATGAGGTGCTTAAAGATTTTTCAGTTCATAACATCTTTGACTAAATCCTCTGGCTCAACT
ATAGCTGCTCGGCTAATTGTCTTAGCAACTATAGCTGCTCGGCTAATTGTCTTAGCAACT
ATAGCTGCTCGGCTAACTGTCTTAGCCCAGCAGTGTTCAACTTGTCATGACTTAGCTTAT
CTTGGTTCAGCTGGTCTTGGTTTAGCTGATATTGGTTCAAATGTT

Lm_g1003.t1-Lp_g999.t1
ATGGCTTTGAATAGCAGTGTCAGATCTACTGCCAAGTTAATCGCTTCTTCTCATTCATCC
CTCTCAAAATCAGTGAGCAGAAGTTTTCATTCCACTGGTGTGAAGAGGATGGGAGGACAT
GGCCATGATGAGCCGTATTACGTTCACGCGAAGCACATGTACAACTTGGACAGGATGAAG
CATCAGGGATTGAAAATGTCCCTCGCGGTGTTCAGTGCTTTCAGCATTGGTGTTGCAGTT
CCTATCTATGCTGTCATTTTCCAGCAAAAGAAGACAGCTTCTGGT
ATGGCTTTGAATAGCAGTGTCAGATCTACTGCCAAGTTAATCGCTTCTTCTCATTCATCC
CTCTCAAAATCAGTGAGCAGAAGTTTTCATTCCACTGGTGTGAAGAGGATGGGAGGACAT
GGCCATGATGAGCCGTATTACGTTCACGCAAAGCACATGTACAACTTGGACAGGATGAAG
CATCAGGGATTGAAAATGTCCCTCGCGGTGTTCACTGCTTTCAGCATTGGTGTTGCAGTT
CCTATCTATGCTGTCATTTTCCAGCAAAAGAAGACAGCTTCTGTT

Thank you.
Rom

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

Although both sequences are of same length, it shows,

Error. The size of two sequences in 'D0001' is not equal.

While it is working in example file. So did i make something wrong at generating the input file?