MafFilter

Contact owners and managers

1–22 of 22

This is the support forum for the MafFilter software (http://biopp.univ-montp2.fr/forge/maffilter):

- Question regarding the use of MafFilter

- Help needed with MafFilter

- Feature requests...

0 selected

Greg Owens

4/17/25

not outputting all alignment blocks

Hi, I've been starting to use maffilter. I'm testing it on a maf file produced from cactus

unread,

not outputting all alignment blocks

Hi, I've been starting to use maffilter. I'm testing it on a maf file produced from cactus

4/17/25

于振朋, Julien Y. Dutheil7

5/26/22

Q&A

maffiter with compression file error

The MAFs should be sort by maf_sort. 在2020年6月29日星期一 UTC+8 03:52:38<jy.du...@gmail.com> 写道：

unread,

Q&A

maffiter with compression file error

The MAFs should be sort by maf_sort. 在2020年6月29日星期一 UTC+8 03:52:38<jy.du...@gmail.com> 写道：

5/26/22

于振朋, Julien Y. Dutheil2

11/24/20

ExtractFeature

Hi, Have a look at this book chapter: https://link.springer.com/protocol/10.1007/978-1-0716-0199-0_2

unread,

ExtractFeature

Hi, Have a look at this book chapter: https://link.springer.com/protocol/10.1007/978-1-0716-0199-0_2

11/24/20

Yudi Zhang, Julien Y. Dutheil4

6/27/20

Q&A

Extract unique mapped blocks and compile error

Hi, Sorry, I'm only seeing this now... ucsc-maffilter is a distinct program, unrelated to

unread,

Q&A

Extract unique mapped blocks and compile error

Hi, Sorry, I'm only seeing this now... ucsc-maffilter is a distinct program, unrelated to

6/27/20

于振朋, Julien Y. Dutheil2

7/5/19

Q&A

maffilter install failed

Hi, In order to understand what's going wrong, I would need to know: - Which OS you are using -

unread,

Q&A

maffilter install failed

Hi, In order to understand what's going wrong, I would need to know: - Which OS you are using -

7/5/19

Karine Durand, Julien Y. Dutheil2

10/23/18

Q&A

how to put an entropy threshold ?

Dear Karine, Very good point, I'm afraid this is currently not (easily) feasible... The entropy

unread,

Q&A

how to put an entropy threshold ?

Dear Karine, Very good point, I'm afraid this is currently not (easily) feasible... The entropy

10/23/18

mkay...@gmail.com, Julien Y. Dutheil4

10/11/18

Q&A

Unable to generate output from ExtractFeature()

Passing by the forum I realized I had not seen your answer... really sorry about that :s is the

unread,

Q&A

Unable to generate output from ExtractFeature()

Passing by the forum I realized I had not seen your answer... really sorry about that :s is the

10/11/18

Marcos Barbeitos, Julien Yann Dutheil4

10/26/17

Q&A

Problems installing Bio++ and MafFilter

Dear Marcos, The Maf format supposes that sequence names are in the form 'species.chr'.

unread,

Q&A

Problems installing Bio++ and MafFilter

Dear Marcos, The Maf format supposes that sequence names are in the form 'species.chr'.

10/26/17

George Gkafas, Julien Yann Dutheil2

8/7/17

Q&A

maffilter use all the available memory

Dear George, Would you mind sending me (off forum) your maf file (or a link to where I may download

unread,

Q&A

maffilter use all the available memory

Dear George, Would you mind sending me (off forum) your maf file (or a link to where I may download

8/7/17

vania fonseca, Julien Yann Dutheil3

8/7/17

Q&A

Empty output files

Yes, sorry, this was just one of the examples I tried but maybe not the best one indeed. In the

unread,

Q&A

Empty output files

Yes, sorry, this was just one of the examples I tried but maybe not the best one indeed. In the

8/7/17

bo...@sheffield.ac.uk, Julien Yann Dutheil2

4/28/17

Q&A

Full Maf to VCF support

Hi, This option actually exists, but is not yet fully tested. VcfOutput can take an additional

unread,

Q&A

Full Maf to VCF support

Hi, This option actually exists, but is not yet fully tested. VcfOutput can take an additional

4/28/17

Ksenia Lavrichenko, Julien Yann Dutheil13

4/26/17

Q&A

BadCharException error running maffilter ExtractFeatures

Dear Ksenia, It looks like you have not updated the Bio++ libraries (in particular bpp-seq-omics)

unread,

Q&A

BadCharException error running maffilter ExtractFeatures

Dear Ksenia, It looks like you have not updated the Bio++ libraries (in particular bpp-seq-omics)

4/26/17

amin saffari, Julien Yann Dutheil2

1/28/17

Q&A

Concatinating/Merge blocks and order of output MAF

Dear Amin, Indeed, in order to compare efficiently blocks with potentially distinct species in

unread,

Q&A

Concatinating/Merge blocks and order of output MAF

Dear Amin, Indeed, in order to compare efficiently blocks with potentially distinct species in

1/28/17

amin saffari, Julien Yann Dutheil3

1/28/17

Q&A

installing mafFilter from the source

Dear Julien, Thanks for your fast hint and sorry for my late reply! your hint accompanied with -

unread,

Q&A

installing mafFilter from the source

Dear Julien, Thanks for your fast hint and sorry for my late reply! your hint accompanied with -

1/28/17

Meritxell Riera Bellés, Julien Yann Dutheil4

7/12/16

Q&A

Extract features from an alignment

Dear Meritxell, The development version is the one from the git repository. If you want, you can send

unread,

Q&A

Extract features from an alignment

Dear Meritxell, The development version is the one from the git repository. If you want, you can send

7/12/16

Meenakshi Bagadia, Julien Yann Dutheil2

7/12/16

Q&A

Extract Synteny Blocks from 46 way multiz alignment maf file

Deae Meenakshi, There is no absolute rule for max_dist, you have to play around with its value and

unread,

Q&A

Extract Synteny Blocks from 46 way multiz alignment maf file

Deae Meenakshi, There is no absolute rule for max_dist, you have to play around with its value and

7/12/16

Robert Fitak, Julien Yann Dutheil2

7/12/16

Q&A

Entropy and Quality filtering

Oups, for some reason I had not seen this message! Entropy is calculated based on the frequencies of

unread,

Q&A

Entropy and Quality filtering

Oups, for some reason I had not seen this message! Entropy is calculated based on the frequencies of

7/12/16

Luana Arch, Robert Fitak2

5/13/16

Q&A

several MAFs

I am not sure how you can have a separate alignment file for each genome? Unless it is a diploid and

unread,

Q&A

several MAFs

I am not sure how you can have a separate alignment file for each genome? Unless it is a diploid and

5/13/16

michael fontaine, Julien Yann Dutheil4

4/17/16

Q&A

count block size with with only non-N's.

This would awesome! Thanks! Michael

unread,

Q&A

count block size with with only non-N's.

This would awesome! Thanks! Michael

4/17/16

Cheng Zou, Julien Yann Dutheil4

11/5/15

Q&A

http://biopp.univ-montp2.fr/forge/maffilter is broken

I cannot reproduce the error... the link works fine from my side :s Can you access the documentation

unread,

Q&A

http://biopp.univ-montp2.fr/forge/maffilter is broken

I cannot reproduce the error... the link works fine from my side :s Can you access the documentation

11/5/15

Robert Fitak, Julien Yann Dutheil2

1/26/15

Q&A

Example Scripts

Dear Robert, Thanks a lot for these examples. Feedback is always welcome. We are extending MafFilter,

unread,

Q&A

Example Scripts

Dear Robert, Thanks a lot for these examples. Feedback is always welcome. We are extending MafFilter,

1/26/15

Zheng Yan, Julien Yann Dutheil2

1/26/15

Q&A

how to filter overlap MAF

Dear Yan, You can do that using the Subset filter, it has a remove_duplicates option (http://biopp.

unread,

Q&A

how to filter overlap MAF

Dear Yan, You can do that using the Subset filter, it has a remove_duplicates option (http://biopp.

1/26/15