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PROGRAM:

NAME


dialign2-2 - Multiple alignment program using the segment-to-segment approach

SYNOPSIS


dialign2-2 [options] [seq_file]

seq_file is the name of the input sequence file; this must be a multiple FASTA file (all
sequences in one file).

DESCRIPTION


dialign2-2 is a program that constructs alignments from gapfree pairs of similar segments
of the sequences. If (possibly) coding nucleic acid sequences are to be aligned, DIALIGN
optionally translates the compared `nucleic acid segments´ to `peptide segments´ according
to the genetic code -- without presupposing any of the three possible reading frames, so
all combinations of reading frames get checked for significant similarity.

By default, DIALIGN creates a single file containing

· An alignment of the input sequences in DIALIGN format.

· The same alignment in FASTA format.

· A sequence tree in PHYLIP format. This tree is constructed by applying the UPGMA
clustering method to the DIALIGN similarity scores. It roughly reflects the different
degrees of similarity among sequences. For detailed phylogenetic analysis, we
recommend the usual methods for phylogenetic reconstruction.

The format of the output files is documented in /usr/share/doc/dialign/USER_GUIDE.gz. The
FASTA, CLUSTALW and MSF output formats are optionally available (see OPTIONS).

OPTIONS


-afc
Creates additional output file "*.afc" containing data of all fragments considered for
alignment. WARNING: this file can be HUGE!

-afc_v
Like "-afc" but verbose: fragments are explicitly printed. WARNING: this file can be
EVEN BIGGER!

-anc
Anchored alignment. Requires a file seq_file.anc containing anchor points.

-cs
If segments are translated, not only the `Watson strand´ but also the `Crick strand´
is looked at.

-cw
Additional output file in CLUSTAL W format.

-ds
`DNA alignment speed up´. Non-translated nucleic acid fragments are taken into account
only if they start with at least two matches. Speeds up DNA alignment at the expense
of sensitivity.

-fa
Additional output file in FASTA format.

-ff
Creates file *.frg containing information about all fragments that are part of the
respective optimal pairwise alignmnets plus information about consistency in the
multiple alignment.

-fn out_file
Output files are named out_file.extension.

-fop
Creates file *.fop containing coordinates of all fragments that are part of the
respective pairwise alignments.

-fsm
Creates file *.fsm containing coordinates of all fragments that are part of the final
alignment

-iw
Overlap weights switched off (by default, overlap weights are used if up to 35
sequences are aligned). This option speeds up the alignment but may lead to reduced
alignment quality.

-lgs
`Long genomic sequences´ - combines the following options: -ma, -thr 2, -lmax 30,
-smin 8, -nta, -ff, -fop, -ff, -cs, -ds, -pst.

-lgs_t
Like "-lgs" but with all segment pairs assessed at the peptide level (rather than
´mixed alignments´ as with the "-lgs" option). Therefore faster than -lgs but not very
sensitive for non-coding regions.

-lmax x
Maximum fragment length = x (default: x = 40 or x = 120 for `translated´ fragments).
Shorter x speeds up the program but may affect alignment quality.

-lo
(Long Output) Additional file *.log with information abut fragments selected for
pairwise alignment and about consistency in multi-alignment proceedure.

-ma
`mixed alignments´ consisting of P-fragments and N-fragments if nucleic acid sequences
are aligned.

-mask
Residues not belonging to selected fragments are replaced by `*´ characters in output
alignment (rather than being printed in lower-case characters)

-mat
Creates file *mat with substitution counts derived from the fragments that have been
selected for alignment.

-mat_thr t
Like "-mat" but only fragments with weight score > t are considered.

-max_link
"Maximum linkage" clustering used to construct sequence tree (instead of UPGMA).

-min_link
"Minimum linkage" clustering used.

-mot
"Motif" option.

-msf
Separate output file in MSF format.

-n
Input sequences are nucleic acid sequences. No translation of fragments.

-nt
Input sequences are nucleic acid sequences and `nucleic acid segments´ are translated
to `peptide segments´.

-nta
`No textual alignment´. Textual alignment suppressed. This option makes sense if other
output files are of intrest -- e.g. the fragment files created with -ff, -fop, -fsm or
-lo.

-o
Fast version, resulting alignments may be slightly different.

-ow
Overlap weights enforced (By default, overlap weights are used only if up to 35
sequences are aligned since calculating overlap weights is time consuming). Warning:
overlap weights generally improve alignment quality but the running time increases in
the order O(n^4) with the number of sequences. This is why, by default, overlap
weights are used only for sequence sets with < 36 sequences.

-pst
"Print status". Creates and updates a file *.sta with information about the current
status of the program run. This option is recommended if large data sets are aligned
since it allows the user to estimate the remaining running time.

-smin x
Minimum similarity value for first residue pair (or codon pair) in fragments. Speeds
up protein alignment or alignment of translated DNA fragments at the expense of
sensitivity.

-stars x
Maximum number of `*´ characters indicating degree of local similarity among
sequences. By default, no stars are used but numbers between 0 and 9, instead.

-stdo
Results written to standard output.

-ta
Standard textual alignment printed (overrides suppression of textual alignments in
special options, e.g. -lgs).

-thr x
Threshold T = x.

-xfr
"Exclude fragments". List of fragments can be specified that are NOT considered for
pairwise alignment.

General remark: If contradictory options are used, subsequent options override previous
ones, e.g.: dialign2-2 -nt -n seq_file runs the program with the "-n" option (no
translation!), while dialign2-2 -n -nt seq_file runs it with the "-nt" option
(translation!).

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