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The
C source code for version 1.2 (last updated:06/25/2009)
is available for download here:
Windows executable and C source code with
makefile
New
Parameters for version 1.2
[markers for clustering] g"markers.txt" [Yes:
add g and markers filename, No: g]
[clustering distance threshold] T0.001
[clustering option] j4 [0:no clustering, 1:by amino acid, 2:by bases
3:only by distance 4:like 1 but post-clustering, 5:like 2 but post,
6:like 3 but post]
Descriptions of the
new variables:
-
Markers
for Clustering: It is used to cluster similar sequences that
share the same amino acids at specific positions (the markers). A
sample markers file is included in the tar file above.
-
Clustering distance threshold: indicates how similar the sequences
should be. The default is 0.001 which is equivalent to approx. 1 in
1000 nucleotide difference that decides whether two sequences are
clustered for similarity (if their distance is less than this
threshold)
-
Clustering Option: Allows the clustering of highly similar sequences
before or after distance calculations. For improved recombination
detection it is recommended to run pre-clustering (removes
sequences), otherwise post-clustering (does not remove sequences).
Parameters from version 1.0
The parameter file contains all the parameter settings. The
parameters in Sliding MinPD as they appear in the parameter file
(vars.txt) are:
[input file] i"in.fas"
[output file] o"out.txt"
[report all distances] d0 [0:No, 1:Yes]
[activate recombination detection] f1 [0:No, 1:Yes]
[recombination detection option] r2 [1:RIP, 2:B-RIP, 3:SB]
[crossover option] c1 [0:many, 1:only one]
[PCC threshold] p0.4
[window size] w200
[step size] s20
[bootstrap recomb. tiebreaker option] t0 [0:No, 1:Yes]
[bootscan seed] e-3
[bootscan threshold] h92
[bootstrap:1/bootknife:0] b0
[substitution model] vTN93 [options: JC69, K2P, TN93]
[gamma shape - rate heterogeneity] a0.5 [a0.5]
[show bootstrap values] k0 [0:No, 1:Yes]
The
program is run with "minpd <vars.txt"
Descriptions of the
variables:
-
Report
All Distances: writes all pairwise distances between
ancestor/descendants to a file
-
Activate
Recombination Detection: This option turns the recombination
detection feature on/off.
-
Recombination
detection: r2 and r3 run the Bootscan methods that require
specification of the bootscan seed, bootscan threshold and bootstrap
or bootknife options values.
-
Crossover
detection: c1 will detect only one crossover, c0 will detect more
than one.
-
PCC
threshold: Specifies the Pearson Correlation Coefficient value used
as a threshold to reduce pool of candidates. A lower value that is
larger than zero decreases number of false positives.
-
Bootscan
tiebreaker option: Bootstrap values may add up to more than 100 when
ancestors with the same distance are present. Use only in
conjunction with crossover option 1.
-
Bootscan
Threshold: A threshold used for r2 and r3 to reduce pool of
candidates.
-
Bootstrap
or Bootknife: Bootstrap is the standard bootstrap method. Bootfknife
(as implemented in an earlier version of RDP2) is a hybrid between a
bootstrap and a jackknife and removes 25% to 50% of sites replacing
them by other randomly picked sites.
-
Substitution
model and gamma shape for distance calculations: These are
required for all recombination detection options. The standard
bootscan builds NJ trees from a distance matrix and therefore also
requires specification of these variable.
-
The
option to "show bootstrap values" is needed to display the bootstrap
values in the network when using the network drawer (see below).
Input File
The
input file should be a set of already aligned
sequences in Fasta format with sequence IDs
containing the
sampling time as a prefix followed by a dot followed by a sequence
identifier. The sequences do not need to appear in (sampling) order.
See sample file "in.fas"
Output File
The
output of Sliding MinPD is a list of the ancestor-descendant relationships
and a collection of trees to build the evolutionary network.
The first part contains a list of four
semicolon-delimited values:
Descendant;Ancestor;Distance;Bootstrap support
The recombinant sequences are shown with the notation
Ancestor=A1|BKP1|A2|BKP2|...|BKPn|An
Where A1 is the left ancestral donor, BKP1 the
first breakpoint position, A2 the ancestral Donor between
breakpoints BKP1 and BKP2, etc. An is
the right-hand ancestral donor.
Network Drawer
The network
can be build with the online network drawer: http://72.17.173.2:800/minpd/
and it is recommended to use smaller scale factors 0.5 instead of
1 with larger alignments. The input file is the output file created by
MinPD.
The network
drawer outputs the file as a FIG graphic file.
Winfig, a free
Windows viewer, can be used to view Fig files. Other viewers can be
found here:
http://homepage.usask.ca/~ijm451/fig/
Old
Version
Version 1.0 is available for download here:
Download C source code
with makefile
Download
command line (DOS) Windows executable
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