1esl-ssdraw(1) Easel Manual esl-ssdraw(1)
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6 esl-ssdraw - create postscript secondary structure diagrams
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10 esl-ssdraw [options] msafile postscript_template postscript_output_file
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14 esl-ssdraw reads an existing template consensus secondary structure di‐
15 agram from postscript_template and creates new postscript diagrams in‐
16 cluding the template structure but with positions colored differently
17 based on alignment statistics such as frequency of gaps per position,
18 average posterior probability per position or information content per
19 position. Additionally, all or some of the aligned sequences can be
20 drawn separately, with nucleotides or posterior probabilities mapped
21 onto the corresponding positions of the consensus structure.
22 The alignment must be in Stockholm format with per-column reference an‐
25 notation (#=GC RF). The sequences in the alignment must be RNA or DNA
26 sequences. The postscript_template file must contain one page that in‐
27 cludes <rflen> consensus nucleotides (positions), where <rflen> is the
28 number of nongap characters in the reference (RF) annotation of the
29 first alignment in msafile. The specific format required in the post‐
30 script_template is described below in the INPUT section. Postscript
31 diagrams will only be created for the first alignment in msafile.
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36 By default (if run with zero command line options), esl-ssdraw will
37 create a six or seven page postscript_output_file, with each page dis‐
38 playing a different alignment statistic. These pages display the align‐
39 ment consensus sequence, information content per position, mutual in‐
40 formation per position, frequency of inserts per position, average
41 length of inserts per position, frequency of deletions (gaps) per posi‐
42 tion, and average posterior probability per position (if posterior
43 probabilites exist in the alignment) If -d is enabled, all of these
44 pages plus additional ones, such as individual sequences (see discus‐
45 sion of --indi below) will be drawn. These pages can be selected to be
46 drawn individually by using the command line options --cons, --info,
47 --mutinfo, --ifreq, --iavglen, --dall, and --prob. The calculation of
48 the statistics for each of these options is discussed below in the de‐
49 scription for each option. Importantly, only so-called 'consensus' po‐
50 sitions of the alignment will be drawn. A consensus position is one
51 that is a nongap nucleotide in the 'reference' annotation of the Stock‐
52 holm alignment (#=GC RF) read from msafile.
53 By default, a consensus sequence for the input alignment will be calcu‐
56 lated and displayed on the alignment statistic diagrams. The consensus
57 sequence is defined as the most common nucleotide at each consensus po‐
58 sition of the alignment. The consensus sequence will not be displayed
59 if the --no-cnt option is used. The --cthresh, --cambig, and --athresh
60 options affect the definition of the consensus sequence as explained
61 below in the descriptions for those options.
62 If the --tabfile <f> option is used, a tab-delimited text file <f> will
65 be created that includes per-position lists of the numerical values for
66 each of the calculated statistics that were drawn to postscript_out‐
67 put_file. Comment lines in <f> are prefixed with a '#' character and
68 explain the meaning of each of the tab-delimited columns and how each
69 of the statistics was calculated.
70 If --indi is used, esl-ssdraw will create diagrams showing each se‐
72 quence in the alignment on a separate page, with aligned nucleotides in
73 their corresponding position in the structure diagram. By default,
74 basepaired nucleotides will be colored based on their basepair type:
75 either Watson-Crick (A:U, U:A, C:G, or G:C), G:U or U:G, or non-canoni‐
76 cal (the other ten possible basepairs). This coloring can be turned off
77 with the --no-bp option. Also by default, nucleotides that differ from
78 the most common nucleotide at each aligned consensus position will be
79 outlined. If the most common nucleotide occurs in more than 75% of se‐
80 quences that do not have a gap at that position, the outline will be
81 bold. Outlining can be turned off with the --no-ol option.
82 With --indi, if the alignment contains posterior probability annotation
85 (#=GR PP), the postscript_output_file will contain an additional page
86 for each sequence drawn with positions colored by the posterior proba‐
87 bility of each aligned nucleotide. No posterior probability pages will
88 be drawn if the --no-pp option is used.
89 esl-ssdraw can also be used to draw 'mask' diagrams which color posi‐
92 tions of the structure one of two colors depending on if they are in‐
93 cluded or excluded by a mask. This is enabled with the --mask-col <f>
94 option. <f> must contain a single line of <rflen> characters, where
95 <rflen> is the the number of nongap RF characters in the alignment. The
96 line must contain only '0' and '1' characters. A '0' at position <x> of
97 the string indicates position <x> is excluded from the mask, and a '1'
98 indicates position <x> is included by the mask. A page comparing the
99 overlap of the <f> mask from --mask-col and another mask in <f2> will
100 be created if the --mask-diff <f2> option is used.
101 If the --mask <f> option is used, positions excluded by the mask in <f>
104 will be drawn differently (as open circles by default) than positions
105 included by the mask. The style of the masked positions can be modified
106 with the --mask-u, --mask-x, and --mask-a options.
107 Finally, two different types of input files can be used to customize
110 output diagrams using the --dfile and --efile options, as described be‐
111 low.
112
117 The postscript_template_file is a postscript file that must be in a
118 very specific format in order for esl-ssdraw to work. The specifics of
119 the format, described below, are likely to change in future versions of
120 esl-ssdraw. The postscript_output_file files generated by esl-ssdraw
121 will not be valid postscript_template_file format (i.e. an output file
122 from esl-ssdraw cannot be used as an postscript_template_file in a sub‐
123 sequent run of the program).
124 An example postscript_template_file ('trna-ssdraw.ps') is included with
127 the Easel distribution in the 'testsuite/' subdirectory of the top-
128 level 'easel' directory.
129 The postscript_template_file is a valid postscript file. It includes
132 postscript commands for drawing a secondary structure. The commands
133 specify x and y coordinates for placing each nucleotide on the page.
134 The postscript_template_file might also contain commands for drawing
135 lines connecting basepaired positions and tick marks indicating every
136 tenth position, though these are not required, as explained below.
137 If you are unfamiliar with the postscript language, it may be useful
140 for you to know that a postscript page is, by default, 612 points wide
141 and 792 points tall. The (0,0) coordinate of a postscript file is at
142 the bottom left corner of the page, (0,792) is the top left, (612,0) is
143 the bottom right, and (612,792) is the top right. esl-ssdraw uses 8
144 point by 8 point cells for drawing positions of the consensus secondary
145 structure. The 'scale' section of the postscript_template_file allows
146 for different 'zoom levels', as described below. Also, it is important
147 to know that postscript lines beginning with '%' are considered com‐
148 ments and do not include postscript commands.
149 An esl-ssdraw postscript_template_file contains n >= 1 pages, each
152 specifying a consensus secondary structure diagram. Each page is delim‐
153 ited by a 'showpage' line in an 'ignore' section (as described below).
154 esl-ssdraw will read all pages of the postscript_template_file and then
155 choose the appropriate one that corresponds with the alignment in
156 msafile based on the consensus (nongap RF) length of the alignment.
157 For an alignment of consensus length <rflen>, the first page of post‐
158 script_template_file that has a structure diagram with consensus length
159 <rflen> will be used as the template structure for the alignment.
160 Each page of postscript_template_file contains blocks of text organized
163 into seven different possible sections. Each section must begin with a
164 single line '% begin <sectionname>' and end with a single line '% end
165 <sectionname>' and have n >= 1 lines in between. On the begin and end
166 lines, there must be at least one space between the '%' and the 'begin'
167 or 'end'. <sectionname> must be one of the following: 'modelname',
168 'legend', 'scale', 'regurgitate', 'ignore', 'text positiontext', 'text
169 nucleotides', 'lines positionticks', or 'lines bpconnects'. The n >=1
170 lines in between the begin and end lines of each section must be in a
171 specific format that differs for each section as described below.
172 Importantly, each page must end with an 'ignore' section that includes
175 a single line 'showpage' between the begin and end lines. This lets
176 esl-ssdraw know that a page has ended and another might follow.
177 Each page of a postscript_template_file must include a single 'model‐
180 name' section. This section must include exactly one line in between
181 its begin and end lines. This line must begin with a '%' character fol‐
182 lowed by a single space. The remainder of the line will be parsed as
183 the model name and will appear on each page of postscript_output_file
184 in the header section. If the name is more than 16 characters, it will
185 be truncated in the output.
186 Each page of a postscript_template_file must include a single 'legend'
189 section. This section must include exactly one line in between its be‐
190 gin and end lines. This line must be formatted as '% <d1> <f1> <f2>
191 <d2> <f3>', where <d1> is an integer specifying the consensus position
192 with relation to which the legend will be placed; <f1> and <f2> specify
193 the x and y axis offsets for the top left corner of the legend relative
194 to the x and y position of consensus position <d1>; <d2> specifies the
195 size of a cell in the legend and <f3> specifies how many extra points
196 should be between the right hand edge of the legend and the end of the
197 page. the offset of the right hand end of the legend . For example, the
198 line '% 34 -40. -30. 12 0.' specfies that the legend be placed 40
199 points to the left and 30 points below the 34th consensus position,
200 that cells appearing in the legend be squares of size 12 points by 12
201 points, and that the right hand side of the legend flush against the
202 right hand edge of the printable page.
203 Each page of a postscript_template_file must include a single 'scale'
206 section. This section must include exactly one line in between its be‐
207 gin and end lines. This line must be formatted as '<f1> <f2> scale',
208 where <f1> and <f2> are both positive real numbers that are identical,
209 for example '1.7 1.7 scale' is valid, but '1.7 2.7 scale' is not. This
210 line is a valid postscript command which specifies the scale or zoom
211 level on the pages in the output. If <f1> and <f2> are '1.0' the de‐
212 fault scale is used for which the total size of the page is 612 points
213 wide and 792 points tall. A scale of 2.0 will reduce this to 306 points
214 wide by 396 points tall. A scale of 0.5 will increase it to 1224 points
215 wide by 1584 points tall. A single cell corresponding to one position
216 of the secondary structure is 8 points by 8 points. For larger RNAs, a
217 scale of less than 1.0 is appropriate (for example, SSU rRNA models
218 (about 1500 nt) use a scale of about 0.6), and for smaller RNAs, a
219 scale of more than 1.0 might be desirable (tRNA (about 70 nt) uses a
220 scale of 1.7). The best way to determine the exact scale to use is
221 trial and error.
222 Each page of a postscript_template_file can include n >= 0 'regurgi‐
225 tate' sections. These sections can include any number of lines. The
226 text in this section will not be parsed by esl-ssdraw but will be in‐
227 cluded in each page of postscript_output_file. The format of the lines
228 in this section must therefore be valid postscript commands. An example
229 of content that might be in a regurgitate section are commands to draw
230 lines and text annotating the anticodon on a tRNA secondary structure
231 diagram.
232 Each page of a postscript_template_file must include at least 1 'ig‐
235 nore' section. One of these sections must include a single line that
236 reads 'showpage'. This section should be placed at the end of each page
237 of the template file. Other ignore sections can include any number of
238 lines. The text in these section will not be parsed by esl-ssdraw nor
239 will it be included in each page of postscript_output_file. An ignore
240 section can contain comments or postscript commands that draw features
241 of the postscript_template_file that are unwanted in the post‐
242 script_output_file.
243 Each page of a postscript_template_file must include a single 'text nu‐
246 cleotides' section. This section must include exactly <rflen> lines,
247 indicating that the consensus secondary structure has exactly <rflen>
248 nucleotide positions. Each line must be of the format '(<c>) <x> <y>
249 moveto show' where <c> is a nucleotide (this can be any character actu‐
250 ally), and <x> and <y> are the coordinates specifying the location of
251 the nucleotide on the page, they should be positive real numbers. The
252 best way to determine what these coordinates should be is manually by
253 trial and error, by inspecting the resulting structure as you add each
254 nucleotide. Note that esl-ssdraw will color an 8 point by 8 point cell
255 for each position, so nucleotides should be placed about 8 points apart
256 from each other.
257 Each page of a postscript_template_file may or may not include a single
260 'text positiontext' section. This section can include n >= 1 lines,
261 each specifying text to be placed next to specific positions of the
262 structure, for example, to number them. Each line must be of the for‐
263 mat '(<s>) <x> <y> moveto show' where <s> is a string of text to place
264 at coordinates (<x>,<y>) of the postscript page. Currently, the best
265 way to determine what these coordinates is manually by trial and error,
266 by inspecting the resulting diagram as you add each line.
267 Each page of a postscript_template_file may or may not include a single
270 'lines positionticks' section. This section can include n >= 1 lines,
271 each specifying the location of a tick mark on the diagram. Each line
272 must be of the format '<x1> <y1> <x2> <y2> moveto show'. A tick mark
273 (line of width 2.0) will be drawn from point (<x1>,<y1>) to point
274 (<x2>,<y2>) on each page of postscript_output_file. Currently, the
275 best way to determine what these coordinates should be is manually by
276 trial and error, by inspecting the resulting diagram as you add each
277 line.
278 Each page of a postscript_template_file may or may not include a single
281 'lines bpconnects' section. This section must include <nbp> lines,
282 where <nbp> is the number of basepairs in the consensus structure of
283 the input msafile annotated as #=GC SS_cons. Each line should connect
284 two basepaired positions in the consensus structure diagram. Each line
285 must be of the format '<x1> <y1> <x2> <y2> moveto show'. A line will be
286 drawn from point (<x1>,<y1>) to point (<x2>,<y2>) on each page of post‐
287 script_output_file. Currently, the best way to determine what these
288 coordinates should be is manually by trial and error, by inspecting the
289 resulting diagram as you add each line.
290
295 The memory required by esl-ssdraw will be equal to roughly the larger
296 of 2 Mb and the size of the first alignment in msafile. If the --small
297 option is used, the memory required will be independent of the align‐
298 ment size. To use --small the alignment must be in Pfam format, a non-
299 interleaved (1 line/seq) version of Stockholm format.
300 If the --indi option is used, the required memory may exceed the size
302 of the alignment by up to ten-fold, and the output postscript_out‐
303 put_file may be up to 50 times larger than the msafile.
304
307 -h Print brief help; includes version number and summary of all
308 options, including expert options.
309 -d Draw the default set of alignment summary diagrams: consensus
312 sequence, information content, mutual information, insert fre‐
313 quency, average insert length, deletion frequency, and average
314 posterior probability (if posterior probability annotation ex‐
315 ists in the alignment). These diagrams are also drawn by default
316 (if zero command line options are used), but using the -d option
317 allows the user to add additional pages, such as individual
318 aligned sequences with --indi.
319 --mask <f>
322 Read the mask from file <f>, and draw positions differently in
323 postscript_output_file depending on whether they are included or
324 excluded by the mask. <f> must contain a single line of length
325 <rflen> with only '0' and '1' characters. <rflen> is the number
326 of nongap characters in the reference (#=GC RF) annotation of
327 the first alignment in msafile A '0' at position <x> of the mask
328 indicates position <x> is excluded by the mask, and a '1' indi‐
329 cates that position <x> is included by the mask.
330 --small
333 Operate in memory saving mode. Without --indi, required RAM will
334 be independent of the size of the alignment in msafile. With
335 --indi, the required RAM will be roughly ten times the size of
336 the alignment in msafile. For --small to work, the alignment
337 must be in Pfam Stockholm (non-interleaved 1 line/seq) format.
338 --rf Add a page to postscript_output_file showing the reference se‐
341 quence from the #=GC RF annotation in msafile. By default,
342 basepaired nucleotides will be colored based on what type of
343 basepair they are. To turn this off, use --no-bp. This page is
344 drawn by default (if zero command-line options are used).
345 --info Add a page to postscript_output_file with consensus (nongap RF)
348 positions colored based on their information content from the
349 alignment. Information content is calculated as 2.0 - H, where
350 H = sum_x p_x log_2 p_x for x in {A,C,G,U}. This page is drawn
351 by default (if zero command-line options are used).
352 --mutinfo
355 Add a page to postscript_output_file with basepaired consensus
356 (nongap RF) positions colored based on the amount of mutual in‐
357 formation they have in the alignment. Mutual information is
358 sum_{x,y} p_{x,y} log_2 ((p_x * p_y) / p_{x,y}, where x and y
359 are the four possible bases A,C,G,U. p_x is the fractions of
360 aligned sequences that have nucleotide x of in the left half (5'
361 half) of the basepair. p_y is the fraction of aligned sequences
362 that have nucleotide y in the position corresponding to the
363 right half (3' half) of the basepair. And p_{x,y} is the frac‐
364 tion of aligned sequences that have basepair x:y. For all p_x,
365 p_y and p{x,y} only sequences that that have a nongap nucleotide
366 at both the left and right half of the basepair are counted.
367 This page is drawn by default (if zero command-line options are
368 used).
369 --ifreq
372 Add a page to postscript_output_file with each consensus (nongap
373 RF) position colored based on the fraction of sequences that
374 span each position that have at least 1 inserted nucleotide af‐
375 ter the position. A sequence s spans consensus position x that
376 is actual alignment position a if s has at least one nongap nu‐
377 cleotide aligned to a position b <= a and at least one nongap
378 nucleotide aligned to a consensus position c >= a. This page is
379 drawn by default (if zero command-line options are used).
380 --iavglen
383 Add a page to postscript_output_file with each consensus (nongap
384 RF) position colored based on average length of insertions that
385 occur after it. The average is calculated as the total number of
386 inserted nucleotides after position x, divided by the number of
387 sequences that have at least 1 inserted nucleotide after posi‐
388 tion x (so the minimum possible average insert length is 1.0).
389 --dall Add a page to postscript_output_file with each consensus (nongap
392 RF) position colored based on the fraction of sequences that
393 have a gap (delete) at the position. This page is drawn by de‐
394 fault (if zero command-line options are used).
395 --dint Add a page to postscript_output_file with each consensus (nongap
398 RF) position colored based on the fraction of sequences that
399 have an internal gap (delete) at the position. An internal gap
400 in a sequence is one that occurs after (5' of) the sequence's
401 first aligned nucleotide and after (3' of) the sequence's final
402 aligned nucleotide. This page is drawn by default (if zero com‐
403 mand-line options are used).
404 --prob Add a page to postscript_output_file with positions colored
407 based on average posterior probability (PP). The alignment must
408 contain #=GR PP annotation for all sequences. PP annotation is
409 converted to numerical PP values as follows: '*' = 0.975, '9' =
410 0.90, '8' = 0.80, '7' = 0.70, '6' = 0.60, '5' = 0.50, '4' =
411 0.40, '3' = 0.30, '2' = 0.20, '1' = 0.10, '0' = 0.025. This
412 page is drawn by default (if zero command-line options are
413 used).
414 --span Add a page to postscript_output_file with consensus (nongap RF)
417 positions colored based on the fraction of sequences that 'span'
418 the position. A sequence s spans consensus position x that is
419 actual alignment position a if s has at least one nongap nucleo‐
420 tide aligned to a position b <= a and at least one nongap nu‐
421 cleotide aligned to a consensus position c >= a. This page is
422 drawn by default (if zero command-line options are used).
423
427 --indi Add a page displaying the aligned nucleotides in their corre‐
428 sponding consensus positions of the structure diagram for each
429 aligned sequence in the alignment. By default, basepaired nu‐
430 cleotides will be colored based on what type of basepair they
431 are. To turn this off, use --no-bp. If posterior probability
432 information (#=GR PP) exists in the alignment, one additional
433 page per sequence will be drawn displaying the posterior proba‐
434 bilities.
435 -f With --indi, force esl-ssdraw to create a diagram, even if it is
438 predicted to be large (> 100 Mb). By default, if the predicted
439 size exceeds 100 Mb, esl-ssdraw will fail with a warning.
440
444 --no-leg
445 Omit the legend on all pages of postscript_output_file.
446 --no-head
449 Omit the header on all pages of postscript_output_file.
450 --no-foot
453 Omit the footer on all pages of postscript_output_file.
454
459 --mask-col
460 With --mask, postscript_output_file will contain exactly 1 page
461 showing positions included by the mask as black squares, and po‐
462 sitions excluded as pink squares.
463 --mask-diff <f>
466 With --mask <f2> and mask-col, postscript_output_file will con‐
467 tain one additional page comparing the mask from <f> and the
468 mask from <f2>. Positions will be colored based on whether they
469 are included by one mask and not the other, excluded by both
470 masks, and included by both masks.
471
475 --no-pp
476 When used in combination with --indi, do not draw posterior
477 probability structure diagrams for each sequence, even if the
478 alignment has PP annotation.
479 --no-bp
482 Do not color basepaired nucleotides based on their basepair
483 type.
484 --no-ol
487 When used in combination with --indi, do not outline nucleotides
488 that differ from the majority rule consensus nucleotide given
489 the alignment.
490 --no-ntpp
493 When used in combination with --indi, do not draw nucleotides on
494 the individual sequence posterior probability diagrams.
495
499 --no-cnt
500 Do not draw consensus nucleotides on alignment statistic dia‐
501 grams (such as information content diagrams). By default, the
502 consensus nucleotide is defined as the most frequent nucleotide
503 in the alignment at the corresponding position. Consensus nu‐
504 cleotides that occur in at least <x> fraction of the aligned se‐
505 quences (that do not contain a gap at the position) are capital‐
506 ized. By default <x> is 0.75, but can be changed with the
507 --cthresh <x> option.
508 --cthresh <x>
511 Specify the threshold for capitalizing consensus nucleotides de‐
512 fined by the majority rule (i.e. when --cambig is not enabled)
513 as <x>.
514 --cambig
517 Change how consensus nucleotides are calculated from majority
518 rule to the least ambiguous IUPAC nucleotide that represents at
519 least <x> fraction of the nongap nucleotides at each consensus
520 position. By default <x> is 0.9, but can be changed with the
521 --athresh <x> option.
522 --athresh <x>
525 With --cambig, specify the threshold for defining consensus nu‐
526 cleotides is the least ambiguous IUPAC nucleotide that repre‐
527 sents at least <x> fraction of the nongap nucleotides at each
528 position.
529
533 --mask-u
534 With --mask, change the style of masked columns to squares.
535 --mask-x
538 With --mask, change the style of masked columns to x's.
539 --mask-a
542 With --mask and --mask-u or --mask-x draw the alternative style
543 of square or 'x' masks.
544
548 --dfile <f>
549 Read the 'draw file' <f> which specifies numerical values for
550 each consensus position in one or more postscript pages. For
551 each page, the draw file must include <rflen>+3 lines (<rflen>
552 is defined in the DESCRIPTION section). The first three lines
553 are special. The following <rflen> 'value lines' each must con‐
554 tain a single number, the numerical value for the corresponding
555 position. The first of the three special lines defines the 'de‐
556 scription' for the page. This should be text that describes what
557 the numerical values refer to for the page. The maximum allow‐
558 able length is roughly 50 characters (the exact maximum length
559 depends on the template file and the program will report an in‐
560 formative error message upon execution if it is exceeded). The
561 second special line defines the 'legend header' line that which
562 will appear immediately above the legend. It has a maximum al‐
563 lowable length of about 30 characters. The third special line
564 per page must contain exactly 7 numbers, which must be in in‐
565 creasing order, each separated by a space. These numbers define
566 the numerical ranges for the six different colors used to draw
567 the consensus positions on the page. The first number defines
568 the minimum value for the first color (blue) and must be less
569 than or equal to the minimum value from the value lines. The
570 second number defines the minimum value for the second color
571 (turquoise). The third, fourth, fifth and sixth numbers define
572 the minimum values for the third, fourth, fifth and sixth colors
573 (light green, yellow, orange, red), and the seventh final number
574 defines the maximum value for red and must be equal to or
575 greater than the maximum value from the value lines. After the
576 <rflen> value lines, there must exist a special line with only
577 '//', signifying the end of a page. The draw file <f> must end
578 with this special '//' line, even if it only includes a single
579 page. A draw file specifying <n> pages should include exactly
580 <n> * (<rflen> + 4) lines.
581 --efile <f>
584 Read the 'expert draw file' <f> which specifies the colors and
585 nucleotides to draw on each consensus position in one or more
586 postscript pages. Unlike with the --dfile option, no legend will
587 be drawn when --efile is used. For each page, the draw file
588 must include <rflen> lines, each with four or five tab-delimited
589 tokens. The first four tokens on line <x> specify the color to
590 paint position <x> and must be real numbers between 0 and 1. The
591 four numbers specify the cyan, magenta, yellow and black values,
592 respectively, in the CMYK color scheme for the postscript file.
593 The fifth token on line <x> specifies which nucleotide to write
594 on position <x> (on top of the colored background). If the fifth
595 token does not exist, no nucleotide will be written. After the
596 <rflen> lines, there must exist a special line with only '//',
597 signifying the end of a page. The expert draw file <f> must end
598 with this special '//' line, even if it only includes a single
599 page. A expert draw file specifying <n> pages should include ex‐
600 actly <n> * (<rflen> + 1) lines.
601 --ifile <f>
604 Read insert information from the file <f>, which may have been
605 created with INFERNAL's cmalign(1) program. The insert informa‐
606 tion in msafile will be ignored and the information from <f>
607 will supersede it. Inserts are columns that are gaps in the ref‐
608 erence (#=GC RF) annotation.
609
615 http://bioeasel.org/
616
619 Copyright (C) 2020 Howard Hughes Medical Institute.
620 Freely distributed under the BSD open source license.
621
624 http://eddylab.org
625Easel 0.48 Nov 2020 esl-ssdraw(1)