# filter.seqs **URL:** \ **Category:** Commands in mothur\ **Created:** [May 29, 2012, 3:15am UTC](https://forum.mothur.org/t/filter-seqs/918 "2012-05-29T03:15:03Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![kimitas](https://avatars.discourse-cdn.com/v4/letter/k/f08c70/32.png) [@kimitas](https://forum.mothur.org/u/kimitas)\ **Post date:** [May 29, 2012, 3:15am UTC](https://forum.mothur.org/t/filter-seqs/918/1 "2012-05-29T03:15:03Z")
Hi there, …when I run : mothur \> filter.seqs(fasta=Lema\_16S\_adults.trim2.unique.good.align, vertical=T, trump=. ) I end up with sequences of 4 base pairs!!!.. Length of filtered alignment: 4 Number of columns removed: 49996 Length of the original alignment: 50000 Number of sequences used to construct filter: 13104 So I run: mothur \> filter.seqs(fasta=Lema\_16S\_adults.trim2.unique.good.align) and I get my sequences again…what is happening?! I decided to use the later one…is this ok?! Length of filtered alignment: 1178 Number of columns removed: 48822 Length of the original alignment: 50000 Number of sequences used to construct filter: 13104 Thanks! kim ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [May 29, 2012, 3:33pm UTC](https://forum.mothur.org/t/filter-seqs/918/2 "2012-05-29T15:33:19Z")
How are you running screen.seqs? Can you send us the output from summary.seqs using the fasta and name file you are giving screen.seqs? ---
**Author:** ![kimitas](https://avatars.discourse-cdn.com/v4/letter/k/f08c70/32.png) [@kimitas](https://forum.mothur.org/u/kimitas)\ **Post date:** [May 30, 2012, 5:42am UTC](https://forum.mothur.org/t/filter-seqs/918/3 "2012-05-30T05:42:18Z")
Hi Pat, thanks, So basically I when I align my sequences I get: mothur \> align.seqs(fasta=Lema\_16S\_adults.trim2.unique.fasta, reference=silva.bacteria.fasta, flip=t) Start End NBases Ambigs Polymer NumSeqs Minimum: 1044 1048 1 0 1 1 2.5%-tile: 1044 3857 30 0 3 351 25%-tile: 1044 6389 279 0 4 3507 Median: 1044 8419 372 0 5 7014 75%-tile: 1044 10303 433 0 5 10520 97.5%-tile:43007 43116 493 0 5 13676 Maximum: 43116 43116 500 0 5 14026 Mean: 3185.6 10294.7 341.795 0 4.67275 # of Seqs: 14026 so I screen like: mothur \> screen.seqs(fasta=Lema\_16S\_adults.trim2.unique.align, name=Lema\_16S\_adults.trim2.names, start=1044) mothur \> summary.seqs() Start End NBases Ambigs Polymer NumSeqs Minimum: 1044 1048 3 0 1 1 2.5%-tile: 1044 3855 155 0 4 328 25%-tile: 1044 6333 297 0 5 3277 Median: 1044 8411 379 0 5 6553 75%-tile: 1044 10261 437 0 5 9829 97.5%-tile:1044 13862 493 0 5 12777 Maximum: 1044 14965 500 0 5 13104 Mean: 1044 8525 358.279 0 4.76389 # of Seqs: 13104 Basically then I had the problem when I do the dist.seqs and the cluster ()..... I ended up making a Phylip distance matrix and the cluster worked.....not really understand what is my back mistake in all that... :roll: Many thanks!!! ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [May 30, 2012, 1:56pm UTC](https://forum.mothur.org/t/filter-seqs/918/4 "2012-05-30T13:56:50Z")
So the earliest a sequence ends is at position 1048 - so you’re keeping sequences that run from 1044 to after 1048 - viola a 4 bp alignment. Instead try this… screen.seqs(fasta=Lema\_16S\_adults.trim2.unique.align, name=Lema\_16S\_adults.trim2.names, start=1044, end=6333) Also, it doesn't look like you're really doing much for quality trimming. Pat ---
**Author:** ![kimitas](https://avatars.discourse-cdn.com/v4/letter/k/f08c70/32.png) [@kimitas](https://forum.mothur.org/u/kimitas)\ **Post date:** [May 31, 2012, 11:32pm UTC](https://forum.mothur.org/t/filter-seqs/918/5 "2012-05-31T23:32:37Z")
Thanks Pat 😃 Now everything works…! I wish I could attend your August workshop as I am quite new in this and really like mother!..unfortunately I am in the other part of the world (Australia)…so a bit far !! Cheers kim