# the installation folder of TESS
jmao@-----------------------------/solexa_tools/TESS/bin$ ls
tessmV11 tessmV11BYM tessmV11noAdm
# the first one
$ ./tessmV11
Typical Usage: tessm -FF -NN -AA -LL -KK -PP -DD -SS -BB
Options can be specified in any order.
Required Options:
-FF: F = File Name of Input Data File
For file name contains spaces, input it as "F".
-NN: N = Number of Individuals
-AA: A = Ploidy (1 = Haploid, 2 = Diploid, ...)
-LL: L = Number of Loci
-KK: K = Number of Clusters
-TT: T = Degree of Trend
-PP: P = sPatial interaction parameter (default: 1.0)
-DD: D = Parameter of Dirichlet Allele Frequency Model (no F-model)
-SS: S = Total Number of Sweeps of MCMC
-BB: B = Burn In Number of Sweeps of MCMC
Optional Options:
-rr: r = Number of Extra Rows in Data File, Default: 0
-cc: c = Number of Extra Columns in Data File, Default: 0
-ii: i = Folder Name of Input Data File, Default: Current Folder
For folder name contains spaces, input it as "i".
-oo: o = Folder Name of Output Result Files, Default: Current Folder
For folder name contains spaces, input it as "o".
-pp: p = Configuration File for Continue from Highest Likelihood Run, Default: NULL
For file name contains spaces, input it as "p".
-dd: d = Number of dummy individuals, Default: 0
-uu: u = Update sigma?
u = y, Yes (Default)
u = n, No
-upup: up = Update Psi?
up = y, Yes
up = n, No (Default)
-xx: x = admiXture parameter, Default: 30.0
-mm: m = Name of file containing map (ascii-raster format) to predict admixture coefficients on (optional)
For file name contains spaces, input it as "m".
-nn: n = number of coordinates to use in regression. Default: 2.
If n = 1, the second coordinate is used. n=0 dis the same as T=0
-ss: s = Shuffle update order for MCMC?
s = y, Yes
s = n, No (Default)
-jj: j = Init the run with Neighbor Joining tree
j = y, Yes
j = n, No (Default)
-gg: g = Name of file containing Geographic distances between individuals (optional)
For file name contains spaces, input it as "g".
-scsc: sc = scale parameter for geographic distances. User predefined value or enter one. Ignored if no geographic distance file is given.
sc = m, Mean distance between individuals (default)
sc = d, meDian distance between individuals
sc = x, maX distance between individuals
sc = value of the scale parameter (e.g. 10.4)
-spsp: sp = SPecial data format: one individual = one row
sp = y, Yes
sp = n, No (Default)
-bsbs: bs = Burn-In Structure, Default: 0
jmao@oka:/ebio/abt6_projects/backup/solexa_tools/TESS/bin$ ls
tessmV11 tessmV11BYM tessmV11noAdm
# the second one
$ ./tessmV11BYM
Typical Usage: tessm -FF -NN -AA -LL -KK -PP -DD -SS -BB
Options can be specified in any order.
Required Options:
-FF: F = File Name of Input Data File
For file name contains spaces, input it as "F".
-NN: N = Number of Individuals
-AA: A = Ploidy (1 = Haploid, 2 = Diploid, ...)
-LL: L = Number of Loci
-KK: K = Number of Clusters
-TT: T = Degree of Trend
-DD: D = Parameter of Dirichlet Allele Frequency Model (no F-model)
-SS: S = Total Number of Sweeps of MCMC
-BB: B = Burn In Number of Sweeps of MCMC
Optional Options:
-rr: r = Number of Extra Rows in Data File, Default: 0
-cc: c = Number of Extra Columns in Data File, Default: 0
-ii: i = Folder Name of Input Data File, Default: Current Folder
For folder name contains spaces, input it as "i".
-oo: o = Folder Name of Output Result Files, Default: Current Folder
For folder name contains spaces, input it as "o".
-pp: p = Configuration File for Continue from Highest Likelihood Run, Default: NULL
-dd: d = Number of dummy individuals, Default: 0
For file name contains spaces, input it as "p".
-uu: u = Update sigma?
u = y, Yes (Default)
u = n, No
-xx: x = admiXture parameter, Default: 30.0
-mm: m = Name of file containing map (ascii-raster format) to predict admixture coefficients on (optional)
For file name contains spaces, input it as "m".
-ss: s = Shuffle update order for MCMC?
s = y, Yes
s = n, No (Default)
-bsbs: bs = Burn-In Structure, Default: 0
-scsc: sc = scale parameter for geographic distances. User predefined value or enter one. Ignored if no geographic distance file is given.
sc = m, Mean distance between individuals (default)
sc = d, meDian distance between individuals
sc = x, maX distance between individuals
sc = value of the scale parameter (e.g. 10.4)
-spsp: sp = SPecial data format: one individual = one row
sp = y, Yes
sp = n, No (Default)
-gg: g = Name of file containing Geographic distances between individuals (optionnal)
For file name contains spaces, input it as "g".
# the last one
$ ./tessmV11noAdm
Typical Usage: tessm -FF -NN -AA -LL -KK -PP -DD -SS -BB
Options can be specified in any order.
Required Options:
-FF: F = File Name of Input Data File
For file name contains spaces, input it as "F".
-NN: N = Number of Individuals
-AA: A = Ploidy (1 = Haploid, 2 = Diploid, ...)
-LL: L = Number of Loci
-KK: K = Number of Clusters
-PP: P = Interaction Parameter of HMRF
-DD: D = Parameter of Dirichlet Allele Frequency Model
-SS: S = Total Number of Sweeps of MCMC
-BB: B = Burn In Number of Sweeps of MCMC
Optional Options:
-rr: r = Number of Extra Rows in Data File, Default: 0
-cc: c = Number of Extra Columns in Data File, Default: 0
-dd: d = Number of Dummy Individuals, Default: 0
-ii: i = Folder Name of Input Data File, Default: Current Folder
For folder name contains spaces, input it as "i".
-jj: j = Init the run with Neighbor Joining tree
j = y, Yes
j = n, No (Default)
-oo: o = Folder Name of Output Result Files, Default: Current Folder
For folder name contains spaces, input it as "o".
-pp: p = Configuration File for Continue from Previous Run, Default: NULL
For file name contains spaces, input it as "p".
-spsp: sp = SPecial data format: one individual = one row
sp = y, Yes
sp = n, No (Default)
-gg: g = Name of file containing Geographic distances between individuals (optional)
For file name contains spaces, input it as "g".
-scsc: sc = scale parameter for geographic distances. User predefined value or enter one. Ignored if no geographic distance file is given.
sc = m, Mean distance between individuals (default)
sc = d, meDian distance between individuals
sc = x, maX distance between individuals
sc = value of the scale parameter (e.g. 10.4)
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