diff --git a/manual-est/images.log b/manual-est/images.log index 2dccee7..988e656 100644 --- a/manual-est/images.log +++ b/manual-est/images.log @@ -1,4 +1,4 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2022.6.15) 15 MAY 2023 14:55 +This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2024.3.15) 13 JUN 2024 09:14 entering extended mode restricted \write18 enabled. %&-line parsing enabled. diff --git a/manual-est/images.pdf b/manual-est/images.pdf index 7bf59da..75c01e4 100644 Binary files a/manual-est/images.pdf and b/manual-est/images.pdf differ diff --git a/manual-est/images.tex b/manual-est/images.tex index feb23b3..071b556 100644 --- a/manual-est/images.tex +++ b/manual-est/images.tex @@ -118,20 +118,20 @@ \else\expandafter\vss\fi}% \providecommand{\selectlanguage}[1]{}% \makeatletter \tracingstats = 1 +\providecommand{\Kappa}{\textrm{K}} +\providecommand{\Eta}{\textrm{H}} \providecommand{\Zeta}{\textrm{Z}} -\providecommand{\Epsilon}{\textrm{E}} -\providecommand{\Tau}{\textrm{T}} +\providecommand{\Nu}{\textrm{N}} +\providecommand{\Omicron}{\textrm{O}} +\providecommand{\Chi}{\textrm{X}} +\providecommand{\Rho}{\textrm{R}} \providecommand{\Iota}{\textrm{J}} \providecommand{\Mu}{\textrm{M}} \providecommand{\omicron}{\textrm{o}} \providecommand{\Alpha}{\textrm{A}} -\providecommand{\Nu}{\textrm{N}} -\providecommand{\Rho}{\textrm{R}} -\providecommand{\Eta}{\textrm{H}} -\providecommand{\Kappa}{\textrm{K}} -\providecommand{\Chi}{\textrm{X}} -\providecommand{\Omicron}{\textrm{O}} +\providecommand{\Epsilon}{\textrm{E}} \providecommand{\Beta}{\textrm{B}} +\providecommand{\Tau}{\textrm{T}} \begin{document} diff --git a/manual-est/index.html b/manual-est/index.html index 6b3320b..2ba3ef9 100644 --- a/manual-est/index.html +++ b/manual-est/index.html @@ -525,13 +525,13 @@

The Pfam HMM library is also required and the install.pl script should take care of it. However, you can manually download it from the appropriate Pfam FTP site. + HREF="https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz">Pfam FTP site. This file needs to be decompressed, either in the default db folder or in any other location, and then it should be formatted with the program hmmpress, which is also part of the HMMER3 package. A valid command sequence could be: 
 $ cd db;
-$ wget ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
+$ wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
 $ gunzip Pfam-A.hmm.gz;
 $ /your/path/hmmer-3.1b2/src/hmmpress Pfam-A.hmm
@@ -2821,7 +2821,7 @@

The command line arguments were:
latex2html manual-est -no_antialias_text -split 0 -dir manual-est -no_navigation -show_section_numbers

-The translation was initiated on 2023-05-15 +The translation was initiated on 2024-06-13

diff --git a/manual-est/manual-est.html b/manual-est/manual-est.html index 6b3320b..2ba3ef9 100644 --- a/manual-est/manual-est.html +++ b/manual-est/manual-est.html @@ -525,13 +525,13 @@

The Pfam HMM library is also required and the install.pl script should take care of it. However, you can manually download it from the appropriate Pfam FTP site. + HREF="https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz">Pfam FTP site. This file needs to be decompressed, either in the default db folder or in any other location, and then it should be formatted with the program hmmpress, which is also part of the HMMER3 package. A valid command sequence could be: 
 $ cd db;
-$ wget ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
+$ wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
 $ gunzip Pfam-A.hmm.gz;
 $ /your/path/hmmer-3.1b2/src/hmmpress Pfam-A.hmm
@@ -2821,7 +2821,7 @@

The command line arguments were:
latex2html manual-est -no_antialias_text -split 0 -dir manual-est -no_navigation -show_section_numbers

-The translation was initiated on 2023-05-15 +The translation was initiated on 2024-06-13

diff --git a/manual/images.log b/manual/images.log index 5a77dcb..a9d3dd7 100644 --- a/manual/images.log +++ b/manual/images.log @@ -1,4 +1,4 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2022.6.15) 15 MAY 2023 14:54 +This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2024.3.15) 13 JUN 2024 09:14 entering extended mode restricted \write18 enabled. %&-line parsing enabled. diff --git a/manual/images.pdf b/manual/images.pdf index 7d7d379..7cb2b5a 100644 Binary files a/manual/images.pdf and b/manual/images.pdf differ diff --git a/manual/images.tex b/manual/images.tex index 374cd86..e388ab3 100644 --- a/manual/images.tex +++ b/manual/images.tex @@ -118,20 +118,20 @@ \else\expandafter\vss\fi}% \providecommand{\selectlanguage}[1]{}% \makeatletter \tracingstats = 1 -\providecommand{\Chi}{\textrm{X}} -\providecommand{\Nu}{\textrm{N}} -\providecommand{\Alpha}{\textrm{A}} -\providecommand{\Rho}{\textrm{R}} +\providecommand{\Eta}{\textrm{H}} \providecommand{\Tau}{\textrm{T}} -\providecommand{\Iota}{\textrm{J}} \providecommand{\Beta}{\textrm{B}} -\providecommand{\Eta}{\textrm{H}} -\providecommand{\Omicron}{\textrm{O}} +\providecommand{\Alpha}{\textrm{A}} +\providecommand{\Zeta}{\textrm{Z}} \providecommand{\omicron}{\textrm{o}} -\providecommand{\Kappa}{\textrm{K}} +\providecommand{\Iota}{\textrm{J}} +\providecommand{\Omicron}{\textrm{O}} +\providecommand{\Rho}{\textrm{R}} \providecommand{\Mu}{\textrm{M}} +\providecommand{\Nu}{\textrm{N}} +\providecommand{\Chi}{\textrm{X}} +\providecommand{\Kappa}{\textrm{K}} \providecommand{\Epsilon}{\textrm{E}} -\providecommand{\Zeta}{\textrm{Z}} \begin{document} diff --git a/manual/index.html b/manual/index.html index ecce12e..b89a8e2 100644 --- a/manual/index.html +++ b/manual/index.html @@ -524,13 +524,13 @@

The Pfam HMM library is also required and the install.pl script should take care of it. However, you can manually download it from the appropriate Pfam FTP site. + HREF="https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz">Pfam FTP site. This file needs to be decompressed, either in the default db folder or in any other location, and then it should be formatted with the program hmmpress, which is also part of the HMMER3 package. A valid command sequence could be: 
 $ cd db;
-$ wget ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
+$ wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
 $ gunzip Pfam-A.hmm.gz;
 $ /your/path/hmmer-3.1b2/src/hmmpress Pfam-A.hmm
@@ -3218,9 +3218,9 @@

-File HOWTOTettelin is a shell script which performs typical uses of get_homologues.pl. -This script can be made executable on the terminal with: $ chmod +x HOWTOTettelin -and then executed with: $ ./HOWTOTettelin +File HOWTOTettelin is a shell script which performs typical uses of get_homologues.pl, +including jobs that require Pfam. This script can be +executed with: $ ./HOWTOTettelin The first task carried out by the script is to download the same GenBank files used in the landmark work of Tettelin and collaborators (PubMed=16172379); afterwards @@ -4171,7 +4171,7 @@

The command line arguments were:
latex2html manual -no_antialias_text -split 0 -dir manual -no_navigation -show_section_numbers

-The translation was initiated on 2023-05-15 +The translation was initiated on 2024-06-13

diff --git a/manual/manual.html b/manual/manual.html index ecce12e..b89a8e2 100644 --- a/manual/manual.html +++ b/manual/manual.html @@ -524,13 +524,13 @@

The Pfam HMM library is also required and the install.pl script should take care of it. However, you can manually download it from the appropriate Pfam FTP site. + HREF="https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz">Pfam FTP site. This file needs to be decompressed, either in the default db folder or in any other location, and then it should be formatted with the program hmmpress, which is also part of the HMMER3 package. A valid command sequence could be: 
 $ cd db;
-$ wget ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
+$ wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz .;
 $ gunzip Pfam-A.hmm.gz;
 $ /your/path/hmmer-3.1b2/src/hmmpress Pfam-A.hmm
@@ -3218,9 +3218,9 @@

-File HOWTOTettelin is a shell script which performs typical uses of get_homologues.pl. -This script can be made executable on the terminal with: $ chmod +x HOWTOTettelin -and then executed with: $ ./HOWTOTettelin +File HOWTOTettelin is a shell script which performs typical uses of get_homologues.pl, +including jobs that require Pfam. This script can be +executed with: $ ./HOWTOTettelin The first task carried out by the script is to download the same GenBank files used in the landmark work of Tettelin and collaborators (PubMed=16172379); afterwards @@ -4171,7 +4171,7 @@

The command line arguments were:
latex2html manual -no_antialias_text -split 0 -dir manual -no_navigation -show_section_numbers

-The translation was initiated on 2023-05-15 +The translation was initiated on 2024-06-13

diff --git a/tutorial/pangenome_tutorial.html b/tutorial/pangenome_tutorial.html index 5afd308..233a670 100644 --- a/tutorial/pangenome_tutorial.html +++ b/tutorial/pangenome_tutorial.html @@ -1,52 +1,39 @@ - + + - + From genomes to pangenomes: understanding variation among individuals and species - - + - - - - - - - - - - - - - + + + + + + + + + + + @@ -1031,9 +1012,6 @@

References