---
name: "mcxalter"
section: "1"
platform: "linux"
package: "mcl"
version: "1:22-282+ds-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mcxalter"
---

# mcxalter(1)

mcxalter - various network transformations

**mcxalter** **\[-imx** \<fname\> (*specify matrix/graph input*)**\]** **\[-abc** \<fname\> (*specify label input*)**\]** **\[-tab** \<fname\> (*use tab file*)**\]** **\[-icl** \<fname\> (*specify cluster input*)**\]** **\[--block** (*use within-cluster edges*)**\]** **\[--blockc** (*use between-cluster edges*)**\]** **\[-o** \<fname\> (*output*)**\]** **\[-tf** spec (*apply tf-spec to input matrix*)**\]**

This utility supplies various transformations of networks.

**-abc** \<fname\> (*label input*)\
 The file name for input that is in label format.

**-imx** \<fname\> (*input matrix*)\
 The file name for input that is in mcl native matrix format.

**-tab** \<fname\> (*use tab file*)\
 This option causes the output to be printed with the labels found in the tab file. With **-abc** this option will, additionally, construct a graph only on the labels found in the tab file. If this option is used in conjunction with **-imx** the tab domain and the matrix domain are required to be identical.

**-icl** \<fname\> (*specify cluster input*)\
 Read in a cluster file for use with either **--block** or **--blockc**.

**--block** (*use within-cluster edges*)\
 Remove between-cluster edges from the network. This is done first, before other transformations take effect.

**--blockc** (*use between-cluster edges*)\
 Remove within-cluster edges from the network. This is done first, before other transformations take effect.

**-tf** \<tf-spec\> (*transform input matrix values*)\
 Transform the input matrix values according to the syntax described in **[mcxio(5)](/mcxio/5.md)**.

**-o** fname (*output file*)\
 Output file.

Stijn van Dongen.

**[mcxio(5)](/mcxio/5.md)**, **[mcx(1)](/mcx/1.md)**, **[mcxsubs(1)](/mcxsubs/1.md)**, and **[mclfamily(7)](/mclfamily/7.md)** for an overview of all the documentation and the utilities in the mcl family.