Correct load data for Run mmod

[OrsonMM]

Dear team mmod:

I can check that different libraries for load data to genind object can alter results of mmod functions

I am used adegenet library for previous analysis and create a DNAbin object.

obj_4 <- fasta2DNAbin("/media/737_alp_llam_end.fa", chunk=10)

 Converting FASTA alignment into a DNAbin object... 


 Finding the size of a single genome... 


 genome size is: 468 nucleotides 

( 2  lines per genome )

 Importing sequences... 
 Forming final object... 

...done.

obj_4
737 DNA sequences in binary format stored in a matrix.

All sequences of same length: 468 

Labels:
B2-A135
E1-A130
F1-A131
B10-A235
B9-A216
C2-A136
...

Base composition:
    a     c     g     t 
0.283 0.283 0.164 0.271 
(Total: 344.92 kb)

Adegenet library have a function to pass DNAbin object to genind object. And Give these result 28 Loci

adegent_library <- DNAbin2genind(obj_4, pop = Pop)
/// GENIND OBJECT /////////

 // 737 individuals; 28 loci; 58 alleles; size: 238.4 Kb

 // Basic content
   @tab:  737 x 58 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 2-3)
   @loc.fac: locus factor for the 58 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 1-1)
   @type:  codom
   @call: DNAbin2genind(x = obj_4, pop = Pop)

 // Optional content
   @pop: population of each individual (group size range: 48-314)

But using convert function of mmod these give me 1 locus

mmod_library <-  as.genind.DNAbin(obj_4, pop = Pop)
/// GENIND OBJECT /////////

 // 737 individuals; 1 locus; 57 alleles; size: 228.3 Kb

 // Basic content
   @tab:  737 x 57 matrix of allele counts
   @loc.n.all: number of alleles per locus (range: 57-57)
   @loc.fac: locus factor for the 57 columns of @tab
   @all.names: list of allele names for each locus
   @ploidy: ploidy of each individual  (range: 1-1)
   @type:  codom
   @call: .local(.Object = .Object, tab = ..1, pop = ..2, ploidy = 1)

 // Optional content
   @pop: population of each individual (group size range: 48-314)

If I run Phi_st_Meirmans function of mmod the results are differents

Phi_st_Meirmans(adegent_library)
$per.locus
          6          15          19          30          31          32          34          35          36          38 
 -1.9153758  -2.1545447  -1.9942762 -26.8815757  -1.9547215   8.6540814  -0.8085354  73.8280912  47.8747794  -0.6461673 
         39          55          59          61          67          69          73          91         126         192 
 -0.6579821  -1.8710735  -1.9347715  -1.9347715   8.7029927  -2.0180501  -1.9347715  -0.5389611   7.0012439  -1.2773257 
        212         218         219         230         231         259         271         284 
  6.1651727  -2.9712335  -2.9370603   9.4423593  -1.9347715  -3.1745577 -14.9206610   7.8309535 

$global
[1] 29.40818

 Phi_st_Meirmans(mmod_library)
$per.locus
       L1 
0.8883799 

$global
[1] 0.8883799

I apreciated your feed back,

PD: For my research actually I am using the as.genind.DNAbin function for run mmod.