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VSEARCH 2.28.1
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@torognes
torognes committed Apr 26, 2024
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38 changes: 19 additions & 19 deletions README.md
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Expand Up @@ -37,7 +37,7 @@ Most of the nucleotide based commands and options in USEARCH version 7 are suppo

## Getting Help

If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion.
If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion.

## Example

Expand All @@ -50,9 +50,9 @@ In the example below, VSEARCH will identify sequences in the file database.fsa t
**Source distribution** To download the source distribution from a [release](https://github.com/torognes/vsearch/releases) and build the executable and the documentation, use the following commands:

```
wget https://github.com/torognes/vsearch/archive/v2.28.0.tar.gz
tar xzf v2.28.0.tar.gz
cd vsearch-2.28.0
wget https://github.com/torognes/vsearch/archive/v2.28.1.tar.gz
tar xzf v2.28.1.tar.gz
cd vsearch-2.28.1
./autogen.sh
./configure CFLAGS="-O3" CXXFLAGS="-O3"
make
Expand Down Expand Up @@ -81,48 +81,48 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v
Download the appropriate executable for your system using the following commands if you are using a Linux x86_64 system:

```sh
wget https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch-2.28.0-linux-x86_64.tar.gz
tar xzf vsearch-2.28.0-linux-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch-2.28.1-linux-x86_64.tar.gz
tar xzf vsearch-2.28.1-linux-x86_64.tar.gz
```

Or these commands if you are using a Linux ppc64le system:

```sh
wget https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch-2.28.0-linux-ppc64le.tar.gz
tar xzf vsearch-2.28.0-linux-ppc64le.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch-2.28.1-linux-ppc64le.tar.gz
tar xzf vsearch-2.28.1-linux-ppc64le.tar.gz
```

Or these commands if you are using a Linux aarch64 (arm64) system:

```sh
wget https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch-2.28.0-linux-aarch64.tar.gz
tar xzf vsearch-2.28.0-linux-aarch64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch-2.28.1-linux-aarch64.tar.gz
tar xzf vsearch-2.28.1-linux-aarch64.tar.gz
```

Or these commands if you are using a Mac with an Apple Silicon CPU:

```sh
wget https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch-2.28.0-macos-aarch64.tar.gz
tar xzf vsearch-2.28.0-macos-aarch64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch-2.28.1-macos-aarch64.tar.gz
tar xzf vsearch-2.28.1-macos-aarch64.tar.gz
```

Or these commands if you are using a Mac with an Intel CPU:

```sh
wget https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch-2.28.0-macos-x86_64.tar.gz
tar xzf vsearch-2.28.0-macos-x86_64.tar.gz
wget https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch-2.28.1-macos-x86_64.tar.gz
tar xzf vsearch-2.28.1-macos-x86_64.tar.gz
```

Or if you are using Windows, download and extract (unzip) the contents of this file:

```
https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch-2.28.0-win-x86_64.zip
https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch-2.28.1-win-x86_64.zip
```

Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.28.0-linux-x86_64` or `vsearch-2.28.0-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed.
Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.28.1-linux-x86_64` or `vsearch-2.28.1-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`. Versions with statically compiled libraries are available for Linux systems. These have "-static" in their name, and could be used on systems that do not have all the necessary libraries installed.

**Windows**: You will now have the binary distribution in a folder
called `vsearch-2.28.0-win-x86_64`. The vsearch executable is called
called `vsearch-2.28.1-win-x86_64`. The vsearch executable is called
`vsearch.exe`. The manual in PDF format is called
`vsearch_manual.pdf`. If you want to be able to call `vsearch.exe`
from any command prompt window, you can put the vsearch executable in
Expand All @@ -135,7 +135,7 @@ and `zlib1.dll` files required for reading compressed input
files. These DLL's have been obtained for mingw-w64 from the MSYS2
platform.

**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.28.0/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.28.1/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).


## Packages, plugins, and wrappers
Expand Down Expand Up @@ -179,7 +179,7 @@ When compiling VSEARCH the header files for the following two optional libraries

VSEARCH will automatically check whether these libraries are available and load them dynamically.

On Windows these libraries are called zlib1.dll and libbz2.dll. These DLL's are included with the released distribution of vsearch 2.28.0 and later.
On Windows these libraries are called zlib1.dll and libbz2.dll. These DLL's are included with the released distribution of vsearch 2.28.1 and later.

To create the PDF file with the manual the ps2pdf tool is required. It is part of the ghostscript package.

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2 changes: 1 addition & 1 deletion configure.ac
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Expand Up @@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.

AC_PREREQ([2.63])
AC_INIT([vsearch], [2.28.0], [[email protected]], [vsearch], [https://github.com/torognes/vsearch])
AC_INIT([vsearch], [2.28.1], [[email protected]], [vsearch], [https://github.com/torognes/vsearch])
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE([subdir-objects])
AC_LANG([C++])
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8 changes: 6 additions & 2 deletions man/vsearch.1
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@@ -1,7 +1,7 @@
.\" import www macros (URL, TAG, MTO)
.mso www.tmac
.\" ============================================================================
.TH vsearch 1 "April 26, 2024" "version 2.28.0" "USER COMMANDS"
.TH vsearch 1 "April 26, 2024" "version 2.28.1" "USER COMMANDS"
.\" ============================================================================
.SH NAME
vsearch \(em a versatile open-source tool for microbiome analysis,
Expand Down Expand Up @@ -4925,7 +4925,11 @@ recommended and will probably soon be the default. Furthermore, a
ninth taxonomic rank, strain (letter t), is now recognized. The speed
of the sintax command has also been significantly improved at least in
some cases. Run vsearch with the randseed option and 1 thread to
ensure reproducibility of the random choices in the algorith.
ensure reproducibility of the random choices in the algorithm.
.TP
.BR v2.28.1\~ "released April 26th, 2024"
Fix a segmentation fault that could occur with the blast6out and
output_no_hits options.
.LP
.\" ============================================================================
.\" TODO:
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