SCaFoS - Command line mode

Selection, Concatenation and Fusion of Sequences

Command line mode

For a detailed description of how to launch SCaFoS according to the operating system, see 'To run SCaFoS' in the Graphical mode section

To create the OTU files

scafos in=<dirIn> out=<dirOut>
[frq=<freq>] [name=<file.nom>] [l=<minlen>]
[cat=yes]

dirIn	directory of input files of aligned sequences
dirOut	output directory
freq	minimum frequency of species in files
file.nom	list of species with corresponding taxa
minlen	minimal percent of sequence length to keep a sequence (default=10%); i.e. minimal length needed to calculate the evolutionary distance or to conserve the chimerical sequence
cat=yes	done an automatic concatenation after creation of OTU file (default=no)

To select files

scafos in=<dirIn> out=<dirOut> file.otu=<file>.otu
o=[ofav] [l=<minlen>]

dirIn	directory of input files of aligned sequences
dirOut	output directory
file.otu	list of OTUs used for assembling datasets
o	write files with ONLY SELECTED SPECIES in dirOut not compatible with f and a options
f	copy files with AT LEAST ONE SELECTED SPECIES in dirOut not compatible with o and a options
a	copy files containing ALL OTUs in dirOut not compatible with f and o options
v	verbose
minlen	minimal percent of sequence length to keep a sequence (default=10%); i.e. minimal length needed to calculate the evolutionary distance or to conserve the chimerical sequence

To construct dataset

scafos in=<dirIn> out=<dirOut>
otu=<file>.otu [gamma=yes] [t=<threshold>]
[puz=no] o=[gsclrv] g=<number>
s=<percent> p=<step>] [def=yes auto=yes]
[m=<missing>] [l=<minlen>]
[format=fpmnba] [color=yes] [cmp=yes]

dirIn	directory of input files of aligned sequences
dirOut	output directory
file.otu	list of OTUs used for assembling datasets
gamma=yes	use of 4 gamma categories to calculate evolutionary distances
threshold	threshold used to compare distances from puzzle and eliminate OTUs containing too divergent sequences (default=25%)
puz=no	doesn't use PUZZLE to determine best sequence (default=use of PUZZLE) not compatible with def option
g	make subdirectories with files containing less than number missing OTUs (default = number of OTUs)
s	make subdirectories of files containing less than percent of missing sites (default = 20%)
c	make chimera with partial sequences in an OTU
l	add character number in concatenated sequence after sequence name
r	remove completely a file when at least one OTU does not respect the threshold (default=no removal action)br> not compatible with def option
v	verbose
step	step of percent of missing sites to create sub-directories (default=5)
def=yes	use of input files *.def for selected sequences (default=sequences selected by SCaFoS computation)
auto=yes	use SCaFoS computation and don't ask user if more than one sequences are possible (default=no)
missing	percent of missing sites to use sequence as a complete sequence [0:50]
minlen	minimal percent of sequence length to keep a sequence; i.e. minimal length needed to calculate the evolutionary distance or to conserve the chimerical sequence (default=10%)
f	output files in FASTA format
p	output files in PHYLIP format
m	output files in MUST format
n	output files in NEXUS format
b	output files in NEXUS format with commands for MrBayes
a	output files in NEXUS format with commands for PAUP
color=yes	modify colors in tree.ps files: green ->chimera blue ->selected sequence grey -> discarded sequence (default=no)
cmp=yes	display the variation in amino acid or nucleotide composition

< Input files

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Hervé PHILIPPE's Lab